Sun 23 Dec 22:23:13 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gvk-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:22 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 296 and 0 Target number of residues in the AU: 296 Target solvent content: 0.6191 Checking the provided sequence file Detected sequence length: 317 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 317 Adjusted target solvent content: 0.59 Input MTZ file: 2gvk-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 182 Cell parameters: 109.180 109.180 122.210 90.000 90.000 120.000 Input sequence file: 2gvk-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2536 target number of atoms Had to go as low as 0.85 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 29.072 3.200 Wilson plot Bfac: 60.98 7532 reflections ( 99.70 % complete ) and 0 restraints for refining 2842 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3267 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2941 (Rfree = 0.000) for 2842 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 2.77 Search for helices and strands: 0 residues in 0 chains, 2908 seeds are put forward Round 1: 214 peptides, 31 chains. Longest chain 14 peptides. Score 0.524 Round 2: 234 peptides, 25 chains. Longest chain 23 peptides. Score 0.659 Round 3: 249 peptides, 22 chains. Longest chain 25 peptides. Score 0.726 Round 4: 239 peptides, 22 chains. Longest chain 27 peptides. Score 0.704 Round 5: 251 peptides, 21 chains. Longest chain 35 peptides. Score 0.740 Taking the results from Round 5 Chains 24, Residues 230, Estimated correctness of the model 73.2 % 2 chains (29 residues) have been docked in sequence Building loops using Loopy2018 24 chains (230 residues) following loop building 2 chains (29 residues) in sequence following loop building ------------------------------------------------------ 7532 reflections ( 99.70 % complete ) and 4382 restraints for refining 2314 atoms. 3360 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2844 (Rfree = 0.000) for 2314 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 2: After refmac, R = 0.2710 (Rfree = 0.000) for 2269 atoms. Found 8 (20 requested) and removed 19 (10 requested) atoms. Cycle 3: After refmac, R = 0.2643 (Rfree = 0.000) for 2239 atoms. Found 10 (19 requested) and removed 14 (10 requested) atoms. Cycle 4: After refmac, R = 0.2627 (Rfree = 0.000) for 2227 atoms. Found 10 (19 requested) and removed 12 (10 requested) atoms. Cycle 5: After refmac, R = 0.2652 (Rfree = 0.000) for 2216 atoms. Found 14 (17 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 2.83 Search for helices and strands: 0 residues in 0 chains, 2286 seeds are put forward Round 1: 224 peptides, 23 chains. Longest chain 37 peptides. Score 0.657 Round 2: 241 peptides, 21 chains. Longest chain 31 peptides. Score 0.719 Round 3: 240 peptides, 18 chains. Longest chain 51 peptides. Score 0.747 Round 4: 243 peptides, 20 chains. Longest chain 27 peptides. Score 0.733 Round 5: 234 peptides, 23 chains. Longest chain 22 peptides. Score 0.682 Taking the results from Round 3 Chains 25, Residues 222, Estimated correctness of the model 74.5 % 5 chains (106 residues) have been docked in sequence Building loops using Loopy2018 25 chains (222 residues) following loop building 5 chains (106 residues) in sequence following loop building ------------------------------------------------------ 7532 reflections ( 99.70 % complete ) and 3889 restraints for refining 2314 atoms. 2599 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2809 (Rfree = 0.000) for 2314 atoms. Found 18 (18 requested) and removed 27 (10 requested) atoms. Cycle 7: After refmac, R = 0.2617 (Rfree = 0.000) for 2290 atoms. Found 16 (18 requested) and removed 11 (10 requested) atoms. Cycle 8: After refmac, R = 0.2480 (Rfree = 0.000) for 2289 atoms. Found 8 (17 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.2385 (Rfree = 0.000) for 2282 atoms. Found 5 (17 requested) and removed 12 (10 requested) atoms. Cycle 10: After refmac, R = 0.2328 (Rfree = 0.000) for 2269 atoms. Found 8 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 2.77 Search for helices and strands: 0 residues in 0 chains, 2336 seeds are put forward Round 1: 247 peptides, 21 chains. Longest chain 33 peptides. Score 0.732 Round 2: 249 peptides, 20 chains. Longest chain 51 peptides. Score 0.745 Round 3: 250 peptides, 18 chains. Longest chain 34 peptides. Score 0.766 Round 4: 248 peptides, 18 chains. Longest chain 56 peptides. Score 0.763 Round 5: 243 peptides, 19 chains. Longest chain 36 peptides. Score 0.743 Taking the results from Round 3 Chains 18, Residues 232, Estimated correctness of the model 77.9 % 3 chains (78 residues) have been docked in sequence Building loops using Loopy2018 18 chains (232 residues) following loop building 3 chains (78 residues) in sequence following loop building ------------------------------------------------------ 7532 reflections ( 99.70 % complete ) and 4045 restraints for refining 2315 atoms. 2823 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2694 (Rfree = 0.000) for 2315 atoms. Found 16 (16 requested) and removed 19 (10 requested) atoms. Cycle 12: After refmac, R = 0.2424 (Rfree = 0.000) for 2300 atoms. Found 9 (16 requested) and removed 14 (10 requested) atoms. Cycle 13: After refmac, R = 0.2318 (Rfree = 0.000) for 2292 atoms. Found 7 (15 requested) and removed 17 (10 requested) atoms. Cycle 14: After refmac, R = 0.2334 (Rfree = 0.000) for 2281 atoms. Found 5 (15 requested) and removed 11 (10 requested) atoms. Cycle 15: After refmac, R = 0.2260 (Rfree = 0.000) for 2272 atoms. Found 11 (14 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.78 Search for helices and strands: 0 residues in 0 chains, 2336 seeds are put forward Round 1: 243 peptides, 25 chains. Longest chain 28 peptides. Score 0.681 Round 2: 250 peptides, 23 chains. Longest chain 47 peptides. Score 0.718 Round 3: 247 peptides, 20 chains. Longest chain 32 peptides. Score 0.742 Round 4: 245 peptides, 19 chains. Longest chain 47 peptides. Score 0.747 Round 5: 242 peptides, 20 chains. Longest chain 32 peptides. Score 0.731 Taking the results from Round 4 Chains 21, Residues 226, Estimated correctness of the model 74.5 % 6 chains (110 residues) have been docked in sequence Building loops using Loopy2018 21 chains (226 residues) following loop building 6 chains (110 residues) in sequence following loop building ------------------------------------------------------ 7532 reflections ( 99.70 % complete ) and 3828 restraints for refining 2315 atoms. 2507 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2780 (Rfree = 0.000) for 2315 atoms. Found 14 (14 requested) and removed 19 (10 requested) atoms. Cycle 17: After refmac, R = 0.2573 (Rfree = 0.000) for 2301 atoms. Found 14 (14 requested) and removed 15 (10 requested) atoms. Cycle 18: After refmac, R = 0.2482 (Rfree = 0.000) for 2290 atoms. Found 7 (13 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.2465 (Rfree = 0.000) for 2284 atoms. Found 6 (13 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.2546 (Rfree = 0.000) for 2276 atoms. Found 10 (12 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 2.77 Search for helices and strands: 0 residues in 0 chains, 2346 seeds are put forward Round 1: 208 peptides, 22 chains. Longest chain 23 peptides. Score 0.627 Round 2: 228 peptides, 25 chains. Longest chain 24 peptides. Score 0.643 Round 3: 240 peptides, 23 chains. Longest chain 21 peptides. Score 0.696 Round 4: 241 peptides, 21 chains. Longest chain 33 peptides. Score 0.719 Round 5: 229 peptides, 20 chains. Longest chain 27 peptides. Score 0.703 Taking the results from Round 4 Chains 22, Residues 220, Estimated correctness of the model 69.1 % 5 chains (98 residues) have been docked in sequence Building loops using Loopy2018 22 chains (220 residues) following loop building 5 chains (98 residues) in sequence following loop building ------------------------------------------------------ 7532 reflections ( 99.70 % complete ) and 4034 restraints for refining 2315 atoms. 2800 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2704 (Rfree = 0.000) for 2315 atoms. Found 12 (12 requested) and removed 25 (10 requested) atoms. Cycle 22: After refmac, R = 0.2487 (Rfree = 0.000) for 2293 atoms. Found 12 (12 requested) and removed 16 (10 requested) atoms. Cycle 23: After refmac, R = 0.2423 (Rfree = 0.000) for 2281 atoms. Found 9 (11 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.2368 (Rfree = 0.000) for 2278 atoms. Found 7 (11 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.2365 (Rfree = 0.000) for 2271 atoms. Found 2 (10 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 2.85 Search for helices and strands: 0 residues in 0 chains, 2304 seeds are put forward Round 1: 235 peptides, 23 chains. Longest chain 39 peptides. Score 0.684 Round 2: 236 peptides, 19 chains. Longest chain 37 peptides. Score 0.729 Round 3: 225 peptides, 22 chains. Longest chain 23 peptides. Score 0.671 Round 4: 235 peptides, 20 chains. Longest chain 34 peptides. Score 0.717 Round 5: 230 peptides, 20 chains. Longest chain 41 peptides. Score 0.706 Taking the results from Round 2 Chains 21, Residues 217, Estimated correctness of the model 71.1 % 2 chains (36 residues) have been docked in sequence Building loops using Loopy2018 21 chains (217 residues) following loop building 2 chains (36 residues) in sequence following loop building ------------------------------------------------------ 7532 reflections ( 99.70 % complete ) and 4475 restraints for refining 2314 atoms. 3477 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2601 (Rfree = 0.000) for 2314 atoms. Found 10 (10 requested) and removed 15 (10 requested) atoms. Cycle 27: After refmac, R = 0.2442 (Rfree = 0.000) for 2303 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.2393 (Rfree = 0.000) for 2298 atoms. Found 9 (10 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2362 (Rfree = 0.000) for 2292 atoms. Found 6 (10 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.2324 (Rfree = 0.000) for 2281 atoms. Found 6 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 2.82 Search for helices and strands: 0 residues in 0 chains, 2350 seeds are put forward Round 1: 227 peptides, 21 chains. Longest chain 23 peptides. Score 0.688 Round 2: 236 peptides, 18 chains. Longest chain 33 peptides. Score 0.739 Round 3: 240 peptides, 19 chains. Longest chain 35 peptides. Score 0.737 Round 4: 228 peptides, 25 chains. Longest chain 22 peptides. Score 0.643 Round 5: 241 peptides, 23 chains. Longest chain 22 peptides. Score 0.698 Taking the results from Round 2 Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save 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intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Chains 20, Residues 218, Estimated correctness of the model 73.0 % 3 chains (47 residues) have been docked in sequence Building loops using Loopy2018 20 chains (218 residues) following loop building 3 chains (47 residues) in sequence following loop building ------------------------------------------------------ 7532 reflections ( 99.70 % complete ) and 4447 restraints for refining 2315 atoms. 3404 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2549 (Rfree = 0.000) for 2315 atoms. Found 10 (10 requested) and removed 15 (10 requested) atoms. Cycle 32: After refmac, R = 0.2404 (Rfree = 0.000) for 2301 atoms. Found 10 (10 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.2362 (Rfree = 0.000) for 2295 atoms. Found 8 (10 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.2316 (Rfree = 0.000) for 2279 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2277 (Rfree = 0.000) for 2276 atoms. Found 2 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 2.78 Search for helices and strands: 0 residues in 0 chains, 2346 seeds are put forward Round 1: 230 peptides, 22 chains. Longest chain 34 peptides. Score 0.683 Round 2: 250 peptides, 21 chains. Longest chain 39 peptides. Score 0.738 Round 3: 237 peptides, 18 chains. Longest chain 43 peptides. Score 0.741 Round 4: 243 peptides, 18 chains. Longest chain 54 peptides. Score 0.753 Round 5: 235 peptides, 20 chains. Longest chain 29 peptides. Score 0.717 Taking the results from Round 4 Chains 21, Residues 225, Estimated correctness of the model 75.6 % 5 chains (127 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 A and 94 A Built loop between residues 253 A and 262 A 18 chains (231 residues) following loop building 3 chains (138 residues) in sequence following loop building ------------------------------------------------------ 7532 reflections ( 99.70 % complete ) and 3443 restraints for refining 2315 atoms. 1992 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2872 (Rfree = 0.000) for 2315 atoms. Found 10 (10 requested) and removed 37 (10 requested) atoms. Cycle 37: After refmac, R = 0.2678 (Rfree = 0.000) for 2272 atoms. Found 10 (10 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.2564 (Rfree = 0.000) for 2259 atoms. Found 8 (10 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.2492 (Rfree = 0.000) for 2250 atoms. Found 6 (10 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.2458 (Rfree = 0.000) for 2242 atoms. Found 5 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.82 Search for helices and strands: 0 residues in 0 chains, 2302 seeds are put forward Round 1: 218 peptides, 23 chains. Longest chain 34 peptides. Score 0.642 Round 2: 225 peptides, 21 chains. Longest chain 36 peptides. Score 0.683 Round 3: 223 peptides, 22 chains. Longest chain 29 peptides. Score 0.666 Round 4: 230 peptides, 26 chains. Longest chain 27 peptides. Score 0.637 Round 5: 226 peptides, 22 chains. Longest chain 34 peptides. Score 0.674 Taking the results from Round 2 Chains 24, Residues 204, Estimated correctness of the model 61.5 % 5 chains (87 residues) have been docked in sequence ------------------------------------------------------ 7532 reflections ( 99.70 % complete ) and 4212 restraints for refining 2315 atoms. 3067 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2690 (Rfree = 0.000) for 2315 atoms. Found 10 (10 requested) and removed 29 (10 requested) atoms. Cycle 42: After refmac, R = 0.2519 (Rfree = 0.000) for 2284 atoms. Found 10 (10 requested) and removed 14 (10 requested) atoms. Cycle 43: After refmac, R = 0.2621 (Rfree = 0.000) for 2273 atoms. Found 10 (10 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.2331 (Rfree = 0.000) for 2262 atoms. Found 2 (10 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.2333 (Rfree = 0.000) for 2252 atoms. Found 5 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 2.78 Search for helices and strands: 0 residues in 0 chains, 2302 seeds are put forward Round 1: 207 peptides, 28 chains. Longest chain 24 peptides. Score 0.544 Round 2: 236 peptides, 20 chains. Longest chain 36 peptides. Score 0.719 Round 3: 213 peptides, 21 chains. Longest chain 24 peptides. Score 0.653 Round 4: 215 peptides, 21 chains. Longest chain 32 peptides. Score 0.658 Round 5: 221 peptides, 21 chains. Longest chain 36 peptides. Score 0.673 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 216, Estimated correctness of the model 69.1 % 4 chains (78 residues) have been docked in sequence Sequence coverage is 35 % Consider running further cycles of model building using 2gvk-3_warpNtrace.pdb as input Building loops using Loopy2018 21 chains (216 residues) following loop building 4 chains (78 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7532 reflections ( 99.70 % complete ) and 4108 restraints for refining 2315 atoms. 2968 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2524 (Rfree = 0.000) for 2315 atoms. Found 0 (10 requested) and removed 6 (10 requested) atoms. Cycle 47: After refmac, R = 0.2460 (Rfree = 0.000) for 2304 atoms. Found 0 (10 requested) and removed 6 (10 requested) atoms. Cycle 48: After refmac, R = 0.2417 (Rfree = 0.000) for 2297 atoms. Found 0 (10 requested) and removed 3 (10 requested) atoms. Cycle 49: After refmac, R = 0.2373 (Rfree = 0.000) for 2292 atoms. TimeTaking 58.5