Sun 23 Dec 22:23:01 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.4-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 22:23:11 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.4-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 290 and 0 Target number of residues in the AU: 290 Target solvent content: 0.6268 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-3.4-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-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2536 target number of atoms Had to go as low as 0.90 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 3.400 Wilson plot Bfac: 64.45 6324 reflections ( 99.65 % complete ) and 0 restraints for refining 2807 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3300 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2714 (Rfree = 0.000) for 2807 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 2.91 Search for helices and strands: 0 residues in 0 chains, 2865 seeds are put forward Round 1: 187 peptides, 29 chains. Longest chain 16 peptides. Score 0.462 Round 2: 225 peptides, 27 chains. Longest chain 19 peptides. Score 0.611 Round 3: 249 peptides, 24 chains. Longest chain 31 peptides. Score 0.705 Round 4: 235 peptides, 23 chains. Longest chain 30 peptides. Score 0.684 Round 5: 227 peptides, 23 chains. Longest chain 24 peptides. Score 0.665 Taking the results from Round 3 Chains 24, Residues 225, Estimated correctness of the model 59.1 % 4 chains (78 residues) have been docked in sequence Building loops using Loopy2018 24 chains (225 residues) following loop building 4 chains (78 residues) in sequence following loop building ------------------------------------------------------ 6324 reflections ( 99.65 % complete ) and 3976 restraints for refining 2315 atoms. 2777 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2758 (Rfree = 0.000) for 2315 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 2: After refmac, R = 0.2594 (Rfree = 0.000) for 2269 atoms. Found 14 (17 requested) and removed 15 (8 requested) atoms. Cycle 3: After refmac, R = 0.2490 (Rfree = 0.000) for 2246 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2435 (Rfree = 0.000) for 2232 atoms. Found 5 (15 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2402 (Rfree = 0.000) for 2218 atoms. Found 4 (15 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 2.91 Search for helices and strands: 0 residues in 0 chains, 2292 seeds are put forward Round 1: 228 peptides, 27 chains. Longest chain 29 peptides. Score 0.619 Round 2: 247 peptides, 23 chains. Longest chain 30 peptides. Score 0.711 Round 3: 252 peptides, 20 chains. Longest chain 29 peptides. Score 0.751 Round 4: 249 peptides, 23 chains. Longest chain 28 peptides. Score 0.716 Round 5: 249 peptides, 14 chains. Longest chain 51 peptides. Score 0.800 Taking the results from Round 5 Chains 18, Residues 235, Estimated correctness of the model 79.9 % 4 chains (68 residues) have been docked in sequence Building loops using Loopy2018 18 chains (235 residues) following loop building 4 chains (68 residues) in sequence following loop building ------------------------------------------------------ 6324 reflections ( 99.65 % complete ) and 4061 restraints for refining 2306 atoms. 2874 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2860 (Rfree = 0.000) for 2306 atoms. Found 15 (15 requested) and removed 32 (8 requested) atoms. Cycle 7: After refmac, R = 0.2644 (Rfree = 0.000) for 2276 atoms. Found 15 (15 requested) and removed 11 (8 requested) atoms. Cycle 8: After refmac, R = 0.2520 (Rfree = 0.000) for 2276 atoms. Found 6 (15 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.2453 (Rfree = 0.000) for 2267 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2417 (Rfree = 0.000) for 2257 atoms. Found 7 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.91 Search for helices and strands: 0 residues in 0 chains, 2312 seeds are put forward Round 1: 230 peptides, 19 chains. Longest chain 27 peptides. Score 0.716 Round 2: 239 peptides, 15 chains. Longest chain 54 peptides. Score 0.774 Round 3: 240 peptides, 21 chains. Longest chain 31 peptides. Score 0.717 Round 4: 237 peptides, 17 chains. Longest chain 69 peptides. Score 0.751 Round 5: 224 peptides, 22 chains. Longest chain 34 peptides. Score 0.669 Taking the results from Round 2 Chains 18, Residues 224, Estimated correctness of the model 74.9 % 3 chains (43 residues) have been docked in sequence Building loops using Loopy2018 18 chains (224 residues) following loop building 3 chains (43 residues) in sequence following loop building ------------------------------------------------------ 6324 reflections ( 99.65 % complete ) and 4371 restraints for refining 2306 atoms. 3338 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2661 (Rfree = 0.000) for 2306 atoms. Found 14 (14 requested) and removed 26 (8 requested) atoms. Cycle 12: After refmac, R = 0.2448 (Rfree = 0.000) for 2291 atoms. Found 7 (13 requested) and removed 10 (8 requested) atoms. Cycle 13: After refmac, R = 0.2371 (Rfree = 0.000) for 2286 atoms. Found 4 (13 requested) and removed 9 (8 requested) atoms. Cycle 14: After refmac, R = 0.2320 (Rfree = 0.000) for 2279 atoms. Found 5 (13 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.2279 (Rfree = 0.000) for 2272 atoms. Found 3 (12 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 2.87 Search for helices and strands: 0 residues in 0 chains, 2319 seeds are put forward Round 1: 228 peptides, 24 chains. Longest chain 19 peptides. Score 0.655 Round 2: 236 peptides, 21 chains. Longest chain 25 peptides. Score 0.708 Round 3: 238 peptides, 21 chains. Longest chain 35 peptides. Score 0.713 Round 4: 218 peptides, 19 chains. Longest chain 30 peptides. Score 0.689 Round 5: 225 peptides, 21 chains. Longest chain 32 peptides. Score 0.683 Taking the results from Round 3 Chains 25, Residues 217, Estimated correctness of the model 61.1 % 3 chains (68 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 141 A 25 chains (219 residues) following loop building 2 chains (77 residues) in sequence following loop building ------------------------------------------------------ 6324 reflections ( 99.65 % complete ) and 4000 restraints for refining 2306 atoms. 2875 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2745 (Rfree = 0.000) for 2306 atoms. Found 12 (12 requested) and removed 31 (8 requested) atoms. Cycle 17: After refmac, R = 0.2527 (Rfree = 0.000) for 2272 atoms. Found 12 (12 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.2414 (Rfree = 0.000) for 2263 atoms. Found 10 (11 requested) and removed 14 (8 requested) atoms. Cycle 19: After refmac, R = 0.2323 (Rfree = 0.000) for 2257 atoms. Found 7 (11 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2260 (Rfree = 0.000) for 2253 atoms. Found 6 (11 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 2.91 Search for helices and strands: 0 residues in 0 chains, 2321 seeds are put forward Round 1: 215 peptides, 19 chains. Longest chain 26 peptides. Score 0.682 Round 2: 227 peptides, 20 chains. Longest chain 43 peptides. Score 0.699 Round 3: 222 peptides, 20 chains. Longest chain 46 peptides. Score 0.687 Round 4: 220 peptides, 17 chains. Longest chain 33 peptides. Score 0.716 Round 5: 223 peptides, 19 chains. Longest chain 42 peptides. Score 0.701 Taking the results from Round 4 Chains 19, Residues 203, Estimated correctness of the model 61.9 % 2 chains (37 residues) have been docked in sequence Building loops using Loopy2018 19 chains (203 residues) following loop building 2 chains (37 residues) in sequence following loop building ------------------------------------------------------ 6324 reflections ( 99.65 % complete ) and 4478 restraints for refining 2306 atoms. 3538 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2576 (Rfree = 0.000) for 2306 atoms. Found 10 (10 requested) and removed 23 (8 requested) atoms. Cycle 22: After refmac, R = 0.2457 (Rfree = 0.000) for 2286 atoms. Found 10 (10 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.2344 (Rfree = 0.000) for 2282 atoms. Found 10 (10 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2272 (Rfree = 0.000) for 2282 atoms. Found 4 (9 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2258 (Rfree = 0.000) for 2275 atoms. Found 9 (9 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 2.92 Search for helices and strands: 0 residues in 0 chains, 2347 seeds are put forward Round 1: 206 peptides, 28 chains. Longest chain 25 peptides. Score 0.541 Round 2: 223 peptides, 19 chains. Longest chain 34 peptides. Score 0.701 Round 3: 230 peptides, 25 chains. Longest chain 29 peptides. Score 0.649 Round 4: 232 peptides, 23 chains. Longest chain 39 peptides. Score 0.677 Round 5: 234 peptides, 23 chains. Longest chain 22 peptides. Score 0.682 Taking the results from Round 2 Chains 23, Residues 204, Estimated correctness of the model 58.1 % 4 chains (64 residues) have been docked in sequence Building loops using Loopy2018 23 chains (204 residues) following loop building 4 chains (64 residues) in sequence following loop building ------------------------------------------------------ 6324 reflections ( 99.65 % complete ) and 4252 restraints for refining 2306 atoms. 3185 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2530 (Rfree = 0.000) for 2306 atoms. Found 8 (8 requested) and removed 22 (8 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2376 (Rfree = 0.000) for 2284 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. Cycle 28: After refmac, R = 0.2302 (Rfree = 0.000) for 2277 atoms. Found 5 (8 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2262 (Rfree = 0.000) for 2267 atoms. Found 5 (8 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.2233 (Rfree = 0.000) for 2260 atoms. Found 3 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 2.93 Search for helices and strands: 0 residues in 0 chains, 2318 seeds are put forward Round 1: 207 peptides, 26 chains. Longest chain 17 peptides. Score 0.572 Round 2: 216 peptides, 19 chains. Longest chain 34 peptides. Score 0.684 Round 3: 218 peptides, 24 chains. Longest chain 38 peptides. Score 0.629 Round 4: 221 peptides, 25 chains. Longest chain 19 peptides. Score 0.625 Round 5: 226 peptides, 26 chains. Longest chain 19 peptides. Score 0.626 Taking the results from Round 2 Chains 20, Residues 197, Estimated correctness of the model 53.7 % 2 chains (52 residues) have been docked in sequence ------------------------------------------------------ 6324 reflections ( 99.65 % complete ) and 4382 restraints for refining 2306 atoms. 3386 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2569 (Rfree = 0.000) for 2306 atoms. Found 8 (8 requested) and removed 20 (8 requested) atoms. Cycle 32: After refmac, R = 0.2387 (Rfree = 0.000) for 2286 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2292 (Rfree = 0.000) for 2284 atoms. Found 5 (8 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.2248 (Rfree = 0.000) for 2275 atoms. Found 4 (8 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.2204 (Rfree = 0.000) for 2270 atoms. Found 0 (8 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 2.91 Search for helices and strands: 0 residues in 0 chains, 2320 seeds are put forward Round 1: 186 peptides, 27 chains. Longest chain 20 peptides. Score 0.489 Round 2: 217 peptides, 23 chains. Longest chain 29 peptides. Score 0.639 Round 3: 226 peptides, 23 chains. Longest chain 29 peptides. Score 0.662 Round 4: 215 peptides, 20 chains. Longest chain 26 peptides. Score 0.670 Round 5: 214 peptides, 22 chains. Longest chain 31 peptides. Score 0.643 Taking the results from Round 4 Chains 23, Residues 195, Estimated correctness of the model 49.8 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 6324 reflections ( 99.65 % complete ) and 4355 restraints for refining 2306 atoms. 3400 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2490 (Rfree = 0.000) for 2306 atoms. Found 8 (8 requested) and removed 14 (8 requested) atoms. Cycle 37: After refmac, R = 0.2320 (Rfree = 0.000) for 2289 atoms. Found 6 (8 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.2255 (Rfree = 0.000) for 2283 atoms. Found 4 (8 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2234 (Rfree = 0.000) for 2279 atoms. Found 2 (8 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2212 (Rfree = 0.000) for 2268 atoms. Found 5 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 2.91 Search for helices and strands: 0 residues in 0 chains, 2333 seeds are put forward Round 1: 192 peptides, 27 chains. Longest chain 17 peptides. Score 0.510 Round 2: 213 peptides, 25 chains. Longest chain 20 peptides. Score 0.603 Round 3: 207 peptides, 22 chains. Longest chain 31 peptides. Score 0.625 Round 4: 217 peptides, 22 chains. Longest chain 19 peptides. Score 0.651 Round 5: 220 peptides, 24 chains. Longest chain 24 peptides. Score 0.635 Taking the results from Round 4 Chains 24, Residues 195, Estimated correctness of the model 44.4 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6324 reflections ( 99.65 % complete ) and 4688 restraints for refining 2305 atoms. 3843 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2580 (Rfree = 0.000) for 2305 atoms. Found 8 (8 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.2365 (Rfree = 0.000) for 2292 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2246 (Rfree = 0.000) for 2288 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.2186 (Rfree = 0.000) for 2283 atoms. Found 3 (8 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2163 (Rfree = 0.000) for 2274 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 2.92 Search for helices and strands: 0 residues in 0 chains, 2341 seeds are put forward Round 1: 191 peptides, 27 chains. Longest chain 18 peptides. Score 0.506 Round 2: 207 peptides, 24 chains. Longest chain 18 peptides. Score 0.599 Round 3: 214 peptides, 24 chains. Longest chain 20 peptides. Score 0.618 Round 4: 204 peptides, 25 chains. Longest chain 30 peptides. Score 0.576 Round 5: 204 peptides, 24 chains. Longest chain 19 peptides. Score 0.590 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 190, Estimated correctness of the model 34.4 % 3 chains (44 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 2gvk-3_warpNtrace.pdb as input Building loops using Loopy2018 26 chains (190 residues) following loop building 3 chains (44 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6324 reflections ( 99.65 % complete ) and 4444 restraints for refining 2306 atoms. 3538 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2404 (Rfree = 0.000) for 2306 atoms. Found 0 (8 requested) and removed 4 (8 requested) atoms. Cycle 47: After refmac, R = 0.2325 (Rfree = 0.000) for 2293 atoms. Found 0 (8 requested) and removed 0 (8 requested) atoms. Cycle 48: After refmac, R = 0.2278 (Rfree = 0.000) for 2291 atoms. Found 0 (8 requested) and removed 4 (8 requested) atoms. Cycle 49: After refmac, R = 0.2261 (Rfree = 0.000) for 2284 atoms. TimeTaking 55.43