Sun 23 Dec 22:22:55 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 1vkb-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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/1vkb-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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 22:23:04 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/1vkb-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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 140 and 0 Target number of residues in the AU: 140 Target solvent content: 0.5835 Checking the provided sequence file Detected sequence length: 161 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 161 Adjusted target solvent content: 0.52 Input MTZ file: 1vkb-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: 170 Cell parameters: 85.745 85.745 42.858 90.000 90.000 120.000 Input sequence file: 1vkb-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1288 target number of atoms Had to go as low as 0.70 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: 74.257 3.200 Wilson plot Bfac: 45.30 3072 reflections ( 99.93 % complete ) and 0 restraints for refining 1424 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3659 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3320 (Rfree = 0.000) for 1424 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.91 2.83 Search for helices and strands: 0 residues in 0 chains, 1425 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 8 peptides. Score 0.260 Round 2: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.386 Round 3: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.416 Round 4: 80 peptides, 12 chains. Longest chain 12 peptides. Score 0.474 Round 5: 83 peptides, 13 chains. Longest chain 11 peptides. Score 0.463 Taking the results from Round 4 Chains 12, Residues 68, Estimated correctness of the model 2.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.93 % complete ) and 2700 restraints for refining 1176 atoms. 2440 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3063 (Rfree = 0.000) for 1176 atoms. Found 7 (10 requested) and removed 19 (5 requested) atoms. Cycle 2: After refmac, R = 0.3016 (Rfree = 0.000) for 1162 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 3: After refmac, R = 0.2997 (Rfree = 0.000) for 1158 atoms. Found 9 (10 requested) and removed 10 (5 requested) atoms. Cycle 4: After refmac, R = 0.2966 (Rfree = 0.000) for 1156 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2803 (Rfree = 0.000) for 1156 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.99 2.91 Search for helices and strands: 0 residues in 0 chains, 1179 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.304 Round 2: 63 peptides, 11 chains. Longest chain 11 peptides. Score 0.364 Round 3: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.368 Round 4: 63 peptides, 12 chains. Longest chain 7 peptides. Score 0.323 Round 5: 64 peptides, 10 chains. Longest chain 13 peptides. Score 0.414 Taking the results from Round 5 Chains 10, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.93 % complete ) and 2796 restraints for refining 1176 atoms. 2590 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2866 (Rfree = 0.000) for 1176 atoms. Found 7 (10 requested) and removed 15 (5 requested) atoms. Cycle 7: After refmac, R = 0.2920 (Rfree = 0.000) for 1168 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.2895 (Rfree = 0.000) for 1168 atoms. Found 7 (10 requested) and removed 14 (5 requested) atoms. Cycle 9: After refmac, R = 0.2920 (Rfree = 0.000) for 1161 atoms. Found 5 (10 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.3008 (Rfree = 0.000) for 1153 atoms. Found 5 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.90 2.82 Search for helices and strands: 0 residues in 0 chains, 1175 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.232 Round 2: 64 peptides, 11 chains. Longest chain 12 peptides. Score 0.374 Round 3: 87 peptides, 14 chains. Longest chain 12 peptides. Score 0.460 Round 4: 69 peptides, 10 chains. Longest chain 11 peptides. Score 0.457 Round 5: 69 peptides, 10 chains. Longest chain 13 peptides. Score 0.457 Taking the results from Round 3 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.93 % complete ) and 2720 restraints for refining 1176 atoms. 2442 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2981 (Rfree = 0.000) for 1176 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 12: After refmac, R = 0.2912 (Rfree = 0.000) for 1167 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.2823 (Rfree = 0.000) for 1168 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.2822 (Rfree = 0.000) for 1167 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.2801 (Rfree = 0.000) for 1160 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.93 2.85 Search for helices and strands: 0 residues in 0 chains, 1195 seeds are put forward Round 1: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.364 Round 2: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.315 Round 3: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.365 Round 4: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.415 Round 5: 81 peptides, 14 chains. Longest chain 14 peptides. Score 0.410 Taking the results from Round 4 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.93 % complete ) and 2709 restraints for refining 1176 atoms. 2444 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2786 (Rfree = 0.000) for 1176 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 17: After refmac, R = 0.2853 (Rfree = 0.000) for 1170 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 18: After refmac, R = 0.2708 (Rfree = 0.000) for 1164 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2716 (Rfree = 0.000) for 1165 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2681 (Rfree = 0.000) for 1164 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.92 2.84 Search for helices and strands: 0 residues in 0 chains, 1187 seeds are put forward Round 1: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.309 Round 2: 57 peptides, 10 chains. Longest chain 9 peptides. Score 0.349 Round 3: 57 peptides, 10 chains. Longest chain 9 peptides. Score 0.349 Round 4: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.319 Round 5: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.326 Taking the results from Round 3 Chains 10, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.93 % complete ) and 2902 restraints for refining 1176 atoms. 2724 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2841 (Rfree = 0.000) for 1176 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 22: After refmac, R = 0.2762 (Rfree = 0.000) for 1171 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2898 (Rfree = 0.000) for 1175 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2669 (Rfree = 0.000) for 1174 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2413 (Rfree = 0.000) for 1177 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.97 2.89 Search for helices and strands: 0 residues in 0 chains, 1195 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 11 peptides. Score 0.311 Round 2: 70 peptides, 13 chains. Longest chain 10 peptides. Score 0.349 Round 3: 74 peptides, 15 chains. Longest chain 10 peptides. Score 0.308 Round 4: 71 peptides, 14 chains. Longest chain 7 peptides. Score 0.319 Round 5: 75 peptides, 11 chains. Longest chain 10 peptides. Score 0.470 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 1.4 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.93 % complete ) and 2665 restraints for refining 1176 atoms. 2402 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2694 (Rfree = 0.000) for 1176 atoms. Found 9 (10 requested) and removed 20 (5 requested) atoms. Cycle 27: After refmac, R = 0.2619 (Rfree = 0.000) for 1159 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. Cycle 28: After refmac, R = 0.2585 (Rfree = 0.000) for 1154 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2551 (Rfree = 0.000) for 1157 atoms. Found 8 (10 requested) and removed 13 (5 requested) atoms. Cycle 30: After refmac, R = 0.2475 (Rfree = 0.000) for 1150 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.93 2.85 Search for helices and strands: 0 residues in 0 chains, 1177 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.260 Round 2: 65 peptides, 13 chains. Longest chain 6 peptides. Score 0.302 Round 3: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.383 Round 4: 76 peptides, 12 chains. Longest chain 11 peptides. Score 0.441 Round 5: 71 peptides, 13 chains. Longest chain 7 peptides. Score 0.359 Taking the results from Round 4 Chains 12, Residues 64, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.93 % complete ) and 2525 restraints for refining 1176 atoms. 2223 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2783 (Rfree = 0.000) for 1176 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 32: After refmac, R = 0.2776 (Rfree = 0.000) for 1166 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.2593 (Rfree = 0.000) for 1163 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2565 (Rfree = 0.000) for 1158 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2471 (Rfree = 0.000) for 1153 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.96 2.88 Search for helices and strands: 0 residues in 0 chains, 1171 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.343 Round 2: 65 peptides, 10 chains. Longest chain 10 peptides. Score 0.422 Round 3: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.398 Round 4: 76 peptides, 12 chains. Longest chain 10 peptides. Score 0.441 Round 5: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.389 Taking the results from Round 4 Chains 12, Residues 64, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.93 % complete ) and 2616 restraints for refining 1176 atoms. 2340 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2789 (Rfree = 0.000) for 1176 atoms. Found 8 (10 requested) and removed 14 (5 requested) atoms. Cycle 37: After refmac, R = 0.2624 (Rfree = 0.000) for 1163 atoms. Found 6 (10 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2595 (Rfree = 0.000) for 1154 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2685 (Rfree = 0.000) for 1153 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2716 (Rfree = 0.000) for 1155 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.91 2.83 Search for helices and strands: 0 residues in 0 chains, 1190 seeds are put forward Round 1: 60 peptides, 14 chains. Longest chain 5 peptides. Score 0.209 Round 2: 67 peptides, 12 chains. Longest chain 9 peptides. Score 0.361 Round 3: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.321 Round 4: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.339 Round 5: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.326 Taking the results from Round 2 Chains 12, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.93 % complete ) and 2785 restraints for refining 1176 atoms. 2577 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2821 (Rfree = 0.000) for 1176 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.2560 (Rfree = 0.000) for 1175 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.2591 (Rfree = 0.000) for 1177 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2497 (Rfree = 0.000) for 1180 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2650 (Rfree = 0.000) for 1183 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 2.91 Search for helices and strands: 0 residues in 0 chains, 1211 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.190 Round 2: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.336 Round 3: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.326 Round 4: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.326 Round 5: 54 peptides, 11 chains. Longest chain 12 peptides. Score 0.276 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 49, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 1vkb-3_warpNtrace.pdb as input Building loops using Loopy2018 11 chains (49 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3072 reflections ( 99.93 % complete ) and 2696 restraints for refining 1176 atoms. 2487 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2696 (Rfree = 0.000) for 1176 atoms. Found 0 (10 requested) and removed 4 (5 requested) atoms. Cycle 47: After refmac, R = 0.2772 (Rfree = 0.000) for 1170 atoms. Found 0 (10 requested) and removed 1 (5 requested) atoms. Cycle 48: After refmac, R = 0.2788 (Rfree = 0.000) for 1166 atoms. Found 0 (10 requested) and removed 1 (5 requested) atoms. Cycle 49: After refmac, R = 0.2664 (Rfree = 0.000) for 1165 atoms. Found 0 (10 requested) and removed 1 (5 requested) atoms. Writing output files ... TimeTaking 26.57