null Sun 23 Dec 22:22:49 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 2hti-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hti-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hti-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-3.6-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/2hti-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-3.6-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 22:22:58 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/2hti-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-3.6-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 121 and 0 Target number of residues in the AU: 121 Target solvent content: 0.6629 Checking the provided sequence file Detected sequence length: 185 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 185 Adjusted target solvent content: 0.48 Input MTZ file: 2hti-3.6-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: 178 Cell parameters: 72.007 72.007 129.790 90.000 90.000 120.000 Input sequence file: 2hti-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1480 target number of atoms Had to go as low as 0.45 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: 28.784 3.600 Wilson plot Bfac: 85.81 2572 reflections ( 99.31 % complete ) and 0 restraints for refining 1630 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3336 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3783 (Rfree = 0.000) for 1630 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 1644 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.273 Round 2: 90 peptides, 14 chains. Longest chain 14 peptides. Score 0.469 Round 3: 92 peptides, 12 chains. Longest chain 18 peptides. Score 0.547 Round 4: 87 peptides, 8 chains. Longest chain 22 peptides. Score 0.634 Round 5: 89 peptides, 10 chains. Longest chain 16 peptides. Score 0.588 Taking the results from Round 4 Chains 8, Residues 79, Estimated correctness of the model 27.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2572 reflections ( 99.31 % complete ) and 2667 restraints for refining 1131 atoms. 2359 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3233 (Rfree = 0.000) for 1131 atoms. Found 7 (7 requested) and removed 18 (3 requested) atoms. Cycle 2: After refmac, R = 0.2876 (Rfree = 0.000) for 1100 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. Cycle 3: After refmac, R = 0.2853 (Rfree = 0.000) for 1084 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2820 (Rfree = 0.000) for 1073 atoms. Found 3 (6 requested) and removed 10 (3 requested) atoms. Cycle 5: After refmac, R = 0.2546 (Rfree = 0.000) for 1061 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 1103 seeds are put forward Round 1: 78 peptides, 11 chains. Longest chain 14 peptides. Score 0.479 Round 2: 90 peptides, 9 chains. Longest chain 24 peptides. Score 0.623 Round 3: 90 peptides, 8 chains. Longest chain 18 peptides. Score 0.651 Round 4: 93 peptides, 9 chains. Longest chain 18 peptides. Score 0.641 Round 5: 92 peptides, 8 chains. Longest chain 22 peptides. Score 0.662 Taking the results from Round 5 Chains 9, Residues 84, Estimated correctness of the model 37.3 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2572 reflections ( 99.31 % complete ) and 1972 restraints for refining 1048 atoms. 1558 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2810 (Rfree = 0.000) for 1048 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.2721 (Rfree = 0.000) for 1036 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2677 (Rfree = 0.000) for 1029 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.2662 (Rfree = 0.000) for 1026 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2667 (Rfree = 0.000) for 1016 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 1063 seeds are put forward Round 1: 81 peptides, 11 chains. Longest chain 17 peptides. Score 0.501 Round 2: 91 peptides, 11 chains. Longest chain 18 peptides. Score 0.571 Round 3: 91 peptides, 10 chains. Longest chain 17 peptides. Score 0.600 Round 4: 90 peptides, 8 chains. Longest chain 23 peptides. Score 0.651 Round 5: 87 peptides, 9 chains. Longest chain 20 peptides. Score 0.605 Taking the results from Round 4 Chains 10, Residues 82, Estimated correctness of the model 33.5 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2572 reflections ( 99.31 % complete ) and 2194 restraints for refining 1060 atoms. 1832 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2989 (Rfree = 0.000) for 1060 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 12: After refmac, R = 0.2730 (Rfree = 0.000) for 1050 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2602 (Rfree = 0.000) for 1043 atoms. Found 0 (6 requested) and removed 9 (3 requested) atoms. Cycle 14: After refmac, R = 0.2536 (Rfree = 0.000) for 1030 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.2468 (Rfree = 0.000) for 1026 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 1068 seeds are put forward Round 1: 65 peptides, 9 chains. Longest chain 13 peptides. Score 0.448 Round 2: 84 peptides, 9 chains. Longest chain 23 peptides. Score 0.586 Round 3: 88 peptides, 9 chains. Longest chain 20 peptides. Score 0.611 Round 4: 86 peptides, 9 chains. Longest chain 18 peptides. Score 0.598 Round 5: 88 peptides, 8 chains. Longest chain 24 peptides. Score 0.640 Taking the results from Round 5 Chains 8, Residues 80, Estimated correctness of the model 29.6 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 2572 reflections ( 99.31 % complete ) and 2232 restraints for refining 1127 atoms. 1821 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3051 (Rfree = 0.000) for 1127 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 17: After refmac, R = 0.2848 (Rfree = 0.000) for 1112 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 18: After refmac, R = 0.2620 (Rfree = 0.000) for 1099 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.2611 (Rfree = 0.000) for 1086 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2500 (Rfree = 0.000) for 1077 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 1135 seeds are put forward Round 1: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.403 Round 2: 83 peptides, 7 chains. Longest chain 25 peptides. Score 0.639 Round 3: 90 peptides, 11 chains. Longest chain 21 peptides. Score 0.564 Round 4: 94 peptides, 11 chains. Longest chain 20 peptides. Score 0.590 Round 5: 90 peptides, 10 chains. Longest chain 22 peptides. Score 0.594 Taking the results from Round 2 Chains 8, Residues 76, Estimated correctness of the model 29.3 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 2572 reflections ( 99.31 % complete ) and 2228 restraints for refining 1137 atoms. 1833 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2610 (Rfree = 0.000) for 1137 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 22: After refmac, R = 0.2685 (Rfree = 0.000) for 1122 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 23: After refmac, R = 0.2793 (Rfree = 0.000) for 1103 atoms. Found 5 (7 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.2430 (Rfree = 0.000) for 1081 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 25: After refmac, R = 0.2512 (Rfree = 0.000) for 1074 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 1116 seeds are put forward Round 1: 70 peptides, 11 chains. Longest chain 10 peptides. Score 0.415 Round 2: 76 peptides, 11 chains. Longest chain 12 peptides. Score 0.463 Round 3: 74 peptides, 10 chains. Longest chain 14 peptides. Score 0.483 Round 4: 82 peptides, 10 chains. Longest chain 15 peptides. Score 0.541 Round 5: 86 peptides, 11 chains. Longest chain 14 peptides. Score 0.537 Taking the results from Round 4 Chains 10, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2572 reflections ( 99.31 % complete ) and 2443 restraints for refining 1093 atoms. 2165 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2584 (Rfree = 0.000) for 1093 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 27: After refmac, R = 0.2895 (Rfree = 0.000) for 1085 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 28: After refmac, R = 0.2650 (Rfree = 0.000) for 1068 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 29: After refmac, R = 0.2790 (Rfree = 0.000) for 1058 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 30: After refmac, R = 0.2889 (Rfree = 0.000) for 1049 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 1094 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 13 peptides. Score 0.349 Round 2: 80 peptides, 11 chains. Longest chain 16 peptides. Score 0.494 Round 3: 83 peptides, 11 chains. Longest chain 18 peptides. Score 0.516 Round 4: 90 peptides, 13 chains. Longest chain 19 peptides. Score 0.502 Round 5: 86 peptides, 13 chains. Longest chain 20 peptides. Score 0.472 Taking the results from Round 3 Chains 11, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2572 reflections ( 99.31 % complete ) and 2427 restraints for refining 1121 atoms. 2150 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2603 (Rfree = 0.000) for 1121 atoms. Found 5 (7 requested) and removed 10 (3 requested) atoms. Cycle 32: After refmac, R = 0.2506 (Rfree = 0.000) for 1109 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 33: After refmac, R = 0.2493 (Rfree = 0.000) for 1107 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.2233 (Rfree = 0.000) for 1106 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2137 (Rfree = 0.000) for 1101 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 1160 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 7 peptides. Score 0.301 Round 2: 74 peptides, 10 chains. Longest chain 22 peptides. Score 0.483 Round 3: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.395 Round 4: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.412 Round 5: 78 peptides, 11 chains. Longest chain 15 peptides. Score 0.479 Taking the results from Round 2 Chains 10, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2572 reflections ( 99.31 % complete ) and 2566 restraints for refining 1150 atoms. 2320 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2274 (Rfree = 0.000) for 1150 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2150 (Rfree = 0.000) for 1135 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2438 (Rfree = 0.000) for 1127 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 39: After refmac, R = 0.3281 (Rfree = 0.000) for 1125 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. Cycle 40: After refmac, R = 0.2191 (Rfree = 0.000) for 1111 atoms. Found 5 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 1153 seeds are put forward Round 1: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.369 Round 2: 85 peptides, 14 chains. Longest chain 18 peptides. Score 0.430 Round 3: 83 peptides, 11 chains. Longest chain 19 peptides. Score 0.516 Round 4: 77 peptides, 9 chains. Longest chain 19 peptides. Score 0.538 Round 5: 76 peptides, 10 chains. Longest chain 12 peptides. Score 0.498 Taking the results from Round 4 Chains 9, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2572 reflections ( 99.31 % complete ) and 2589 restraints for refining 1139 atoms. 2326 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2388 (Rfree = 0.000) for 1139 atoms. Found 4 (7 requested) and removed 10 (3 requested) atoms. Cycle 42: After refmac, R = 0.3161 (Rfree = 0.000) for 1126 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 43: After refmac, R = 0.2708 (Rfree = 0.000) for 1114 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.2809 (Rfree = 0.000) for 1102 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 45: After refmac, R = 0.2567 (Rfree = 0.000) for 1097 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 1147 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.278 Round 2: 64 peptides, 9 chains. Longest chain 15 peptides. Score 0.440 Round 3: 72 peptides, 12 chains. Longest chain 13 peptides. Score 0.395 Round 4: 67 peptides, 8 chains. Longest chain 15 peptides. Score 0.499 Round 5: 64 peptides, 9 chains. Longest chain 13 peptides. Score 0.440 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 59, 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 2hti-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2572 reflections ( 99.31 % complete ) and 2527 restraints for refining 1121 atoms. 2299 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2704 (Rfree = 0.000) for 1121 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3065 (Rfree = 0.000) for 1112 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2503 (Rfree = 0.000) for 1107 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2523 (Rfree = 0.000) for 1102 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:17 GMT 2018 Job finished. TimeTaking 28.48 Used memory is bytes: 14802008