Tue 25 Dec 19:27:57 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 2ppv-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-3.8-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/2ppv-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-3.8-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 ============================================================ Tue 25 Dec 19:28:12 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/2ppv-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-3.8-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 288 and 0 Target number of residues in the AU: 288 Target solvent content: 0.6955 Checking the provided sequence file Detected sequence length: 332 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 332 Adjusted target solvent content: 0.65 Input MTZ file: 2ppv-3.8-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: 20 Cell parameters: 133.390 136.620 56.180 90.000 90.000 90.000 Input sequence file: 2ppv-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2656 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: 29.185 3.800 Wilson plot Bfac: 116.01 5295 reflections ( 99.31 % complete ) and 0 restraints for refining 2941 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3607 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3360 (Rfree = 0.000) for 2941 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.94 3.21 Search for helices and strands: 0 residues in 0 chains, 3019 seeds are put forward Round 1: 139 peptides, 24 chains. Longest chain 10 peptides. Score 0.337 Round 2: 172 peptides, 25 chains. Longest chain 15 peptides. Score 0.432 Round 3: 195 peptides, 29 chains. Longest chain 14 peptides. Score 0.448 Round 4: 199 peptides, 24 chains. Longest chain 24 peptides. Score 0.525 Round 5: 204 peptides, 25 chains. Longest chain 16 peptides. Score 0.526 Taking the results from Round 5 Chains 26, Residues 179, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5295 reflections ( 99.31 % complete ) and 5300 restraints for refining 2401 atoms. 4568 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3062 (Rfree = 0.000) for 2401 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 2: After refmac, R = 0.2833 (Rfree = 0.000) for 2337 atoms. Found 10 (13 requested) and removed 20 (6 requested) atoms. Cycle 3: After refmac, R = 0.2949 (Rfree = 0.000) for 2282 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 4: After refmac, R = 0.2822 (Rfree = 0.000) for 2245 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 5: After refmac, R = 0.2875 (Rfree = 0.000) for 2223 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.98 3.24 Search for helices and strands: 0 residues in 0 chains, 2374 seeds are put forward Round 1: 171 peptides, 27 chains. Longest chain 14 peptides. Score 0.401 Round 2: 204 peptides, 22 chains. Longest chain 23 peptides. Score 0.563 Round 3: 194 peptides, 22 chains. Longest chain 19 peptides. Score 0.536 Round 4: 213 peptides, 26 chains. Longest chain 18 peptides. Score 0.538 Round 5: 204 peptides, 24 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 2 Chains 25, Residues 182, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5295 reflections ( 99.31 % complete ) and 4684 restraints for refining 2290 atoms. 3921 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2846 (Rfree = 0.000) for 2290 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 7: After refmac, R = 0.2664 (Rfree = 0.000) for 2231 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 8: After refmac, R = 0.2693 (Rfree = 0.000) for 2198 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.2673 (Rfree = 0.000) for 2173 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.2607 (Rfree = 0.000) for 2150 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.99 3.25 Search for helices and strands: 0 residues in 0 chains, 2294 seeds are put forward Round 1: 187 peptides, 26 chains. Longest chain 16 peptides. Score 0.464 Round 2: 208 peptides, 23 chains. Longest chain 28 peptides. Score 0.561 Round 3: 199 peptides, 23 chains. Longest chain 25 peptides. Score 0.537 Round 4: 198 peptides, 21 chains. Longest chain 38 peptides. Score 0.560 Round 5: 177 peptides, 22 chains. Longest chain 14 peptides. Score 0.489 Taking the results from Round 2 Chains 24, Residues 185, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5295 reflections ( 99.31 % complete ) and 4886 restraints for refining 2290 atoms. 4134 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3003 (Rfree = 0.000) for 2290 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2910 (Rfree = 0.000) for 2243 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 13: After refmac, R = 0.2572 (Rfree = 0.000) for 2203 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 14: After refmac, R = 0.2567 (Rfree = 0.000) for 2182 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.2470 (Rfree = 0.000) for 2167 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.00 3.25 Search for helices and strands: 0 residues in 0 chains, 2311 seeds are put forward Round 1: 171 peptides, 30 chains. Longest chain 9 peptides. Score 0.357 Round 2: 189 peptides, 25 chains. Longest chain 18 peptides. Score 0.483 Round 3: 188 peptides, 23 chains. Longest chain 24 peptides. Score 0.507 Round 4: 205 peptides, 22 chains. Longest chain 23 peptides. Score 0.565 Round 5: 203 peptides, 22 chains. Longest chain 22 peptides. Score 0.560 Taking the results from Round 4 Chains 24, Residues 183, Estimated correctness of the model 0.0 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 5295 reflections ( 99.31 % complete ) and 4652 restraints for refining 2390 atoms. 3765 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2891 (Rfree = 0.000) for 2390 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2905 (Rfree = 0.000) for 2351 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 18: After refmac, R = 0.2800 (Rfree = 0.000) for 2303 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2599 (Rfree = 0.000) for 2272 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2671 (Rfree = 0.000) for 2253 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.02 3.27 Search for helices and strands: 0 residues in 0 chains, 2333 seeds are put forward Round 1: 167 peptides, 27 chains. Longest chain 17 peptides. Score 0.387 Round 2: 183 peptides, 24 chains. Longest chain 21 peptides. Score 0.479 Round 3: 194 peptides, 25 chains. Longest chain 21 peptides. Score 0.498 Round 4: 192 peptides, 25 chains. Longest chain 18 peptides. Score 0.492 Round 5: 203 peptides, 24 chains. Longest chain 22 peptides. Score 0.536 Taking the results from Round 5 Chains 24, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5295 reflections ( 99.31 % complete ) and 5378 restraints for refining 2403 atoms. 4686 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3130 (Rfree = 0.000) for 2403 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 22: After refmac, R = 0.2741 (Rfree = 0.000) for 2365 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 23: After refmac, R = 0.2866 (Rfree = 0.000) for 2331 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 24: After refmac, R = 0.2588 (Rfree = 0.000) for 2306 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2616 (Rfree = 0.000) for 2295 atoms. Found 8 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.97 3.23 Search for helices and strands: 0 residues in 0 chains, 2421 seeds are put forward Round 1: 162 peptides, 28 chains. Longest chain 15 peptides. Score 0.356 Round 2: 187 peptides, 25 chains. Longest chain 19 peptides. Score 0.478 Round 3: 181 peptides, 22 chains. Longest chain 21 peptides. Score 0.500 Round 4: 174 peptides, 20 chains. Longest chain 21 peptides. Score 0.507 Round 5: 167 peptides, 22 chains. Longest chain 19 peptides. Score 0.459 Taking the results from Round 4 Chains 20, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5295 reflections ( 99.31 % complete ) and 5545 restraints for refining 2403 atoms. 4949 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2856 (Rfree = 0.000) for 2403 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2744 (Rfree = 0.000) for 2371 atoms. Found 10 (13 requested) and removed 13 (6 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2758 (Rfree = 0.000) for 2343 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2765 (Rfree = 0.000) for 2321 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2824 (Rfree = 0.000) for 2310 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.01 3.26 Search for helices and strands: 0 residues in 0 chains, 2406 seeds are put forward Round 1: 155 peptides, 29 chains. Longest chain 11 peptides. Score 0.317 Round 2: 163 peptides, 23 chains. Longest chain 16 peptides. Score 0.432 Round 3: 170 peptides, 24 chains. Longest chain 15 peptides. Score 0.440 Round 4: 174 peptides, 22 chains. Longest chain 16 peptides. Score 0.480 Round 5: 170 peptides, 19 chains. Longest chain 18 peptides. Score 0.509 Taking the results from Round 5 Chains 19, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5295 reflections ( 99.31 % complete ) and 5401 restraints for refining 2363 atoms. 4816 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3103 (Rfree = 0.000) for 2363 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 32: After refmac, R = 0.2854 (Rfree = 0.000) for 2312 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 33: After refmac, R = 0.2870 (Rfree = 0.000) for 2298 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 34: After refmac, R = 0.2842 (Rfree = 0.000) for 2279 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.3146 (Rfree = 0.000) for 2271 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.98 3.24 Search for helices and strands: 0 residues in 0 chains, 2385 seeds are put forward Round 1: 142 peptides, 27 chains. Longest chain 9 peptides. Score 0.301 Round 2: 175 peptides, 27 chains. Longest chain 10 peptides. Score 0.413 Round 3: 189 peptides, 24 chains. Longest chain 14 peptides. Score 0.497 Round 4: 181 peptides, 23 chains. Longest chain 14 peptides. Score 0.487 Round 5: 184 peptides, 25 chains. Longest chain 14 peptides. Score 0.469 Taking the results from Round 3 Chains 24, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5295 reflections ( 99.31 % complete ) and 5009 restraints for refining 2309 atoms. 4373 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2671 (Rfree = 0.000) for 2309 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2728 (Rfree = 0.000) for 2275 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 38: After refmac, R = 0.2620 (Rfree = 0.000) for 2250 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 39: After refmac, R = 0.2447 (Rfree = 0.000) for 2231 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2428 (Rfree = 0.000) for 2228 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.98 3.24 Search for helices and strands: 0 residues in 0 chains, 2333 seeds are put forward Round 1: 140 peptides, 25 chains. Longest chain 10 peptides. Score 0.325 Round 2: 156 peptides, 21 chains. Longest chain 20 peptides. Score 0.439 Round 3: 169 peptides, 21 chains. Longest chain 21 peptides. Score 0.479 Round 4: 164 peptides, 20 chains. Longest chain 21 peptides. Score 0.478 Round 5: 173 peptides, 23 chains. Longest chain 21 peptides. Score 0.463 Taking the results from Round 3 Chains 22, Residues 148, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5295 reflections ( 99.31 % complete ) and 5069 restraints for refining 2333 atoms. 4469 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2959 (Rfree = 0.000) for 2333 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2829 (Rfree = 0.000) for 2307 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 43: After refmac, R = 0.2466 (Rfree = 0.000) for 2281 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2552 (Rfree = 0.000) for 2263 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 45: After refmac, R = 0.2533 (Rfree = 0.000) for 2254 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.97 3.23 Search for helices and strands: 0 residues in 0 chains, 2364 seeds are put forward Round 1: 155 peptides, 28 chains. Longest chain 20 peptides. Score 0.332 Round 2: 169 peptides, 24 chains. Longest chain 17 peptides. Score 0.437 Round 3: 164 peptides, 27 chains. Longest chain 12 peptides. Score 0.378 Round 4: 171 peptides, 22 chains. Longest chain 19 peptides. Score 0.471 Round 5: 172 peptides, 23 chains. Longest chain 17 peptides. Score 0.460 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ppv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5295 reflections ( 99.31 % complete ) and 5260 restraints for refining 2376 atoms. 4686 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2608 (Rfree = 0.000) for 2376 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2781 (Rfree = 0.000) for 2350 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2568 (Rfree = 0.000) for 2325 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2353 (Rfree = 0.000) for 2312 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:28:04 GMT 2018 Job finished. TimeTaking 60.11