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 1vk9-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.8-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/1vk9-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.8-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 ============================================================ Sun 23 Dec 22:22:59 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/1vk9-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.8-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 211 and 0 Target number of residues in the AU: 211 Target solvent content: 0.6627 Checking the provided sequence file Detected sequence length: 151 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 151 Adjusted target solvent content: 0.76 Input MTZ file: 1vk9-3.8-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: 180 Cell parameters: 132.922 132.922 66.385 90.000 90.000 120.000 Input sequence file: 1vk9-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1208 target number of atoms Had to go as low as 1.40 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: 115.114 3.800 Wilson plot Bfac: 86.61 3699 reflections ( 99.92 % complete ) and 0 restraints for refining 1424 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.3569 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3396 (Rfree = 0.000) for 1424 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 2.55 Search for helices and strands: 0 residues in 0 chains, 1444 seeds are put forward Round 1: 87 peptides, 12 chains. Longest chain 14 peptides. Score 0.403 Round 2: 107 peptides, 14 chains. Longest chain 21 peptides. Score 0.455 Round 3: 116 peptides, 12 chains. Longest chain 20 peptides. Score 0.536 Round 4: 102 peptides, 10 chains. Longest chain 25 peptides. Score 0.518 Round 5: 116 peptides, 13 chains. Longest chain 27 peptides. Score 0.516 Taking the results from Round 3 Chains 13, Residues 104, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3699 reflections ( 99.92 % complete ) and 2322 restraints for refining 1111 atoms. 1880 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3204 (Rfree = 0.000) for 1111 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.3014 (Rfree = 0.000) for 1096 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 3: After refmac, R = 0.2868 (Rfree = 0.000) for 1082 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 4: After refmac, R = 0.2783 (Rfree = 0.000) for 1073 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.2731 (Rfree = 0.000) for 1073 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 2.53 Search for helices and strands: 0 residues in 0 chains, 1116 seeds are put forward Round 1: 112 peptides, 11 chains. Longest chain 17 peptides. Score 0.539 Round 2: 112 peptides, 13 chains. Longest chain 20 peptides. Score 0.498 Round 3: 115 peptides, 10 chains. Longest chain 32 peptides. Score 0.571 Round 4: 117 peptides, 11 chains. Longest chain 30 peptides. Score 0.559 Round 5: 119 peptides, 11 chains. Longest chain 27 peptides. Score 0.567 Taking the results from Round 3 Chains 12, Residues 105, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3699 reflections ( 99.92 % complete ) and 1971 restraints for refining 1093 atoms. 1471 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2962 (Rfree = 0.000) for 1093 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.2829 (Rfree = 0.000) for 1069 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.2682 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 9: After refmac, R = 0.2627 (Rfree = 0.000) for 1060 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2643 (Rfree = 0.000) for 1059 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 2.58 Search for helices and strands: 0 residues in 0 chains, 1132 seeds are put forward Round 1: 111 peptides, 14 chains. Longest chain 19 peptides. Score 0.473 Round 2: 113 peptides, 12 chains. Longest chain 25 peptides. Score 0.523 Round 3: 107 peptides, 11 chains. Longest chain 19 peptides. Score 0.518 Round 4: 111 peptides, 12 chains. Longest chain 21 peptides. Score 0.515 Round 5: 97 peptides, 12 chains. Longest chain 22 peptides. Score 0.452 Taking the results from Round 2 Chains 12, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3699 reflections ( 99.92 % complete ) and 2319 restraints for refining 1093 atoms. 1927 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2667 (Rfree = 0.000) for 1093 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 12: After refmac, R = 0.2776 (Rfree = 0.000) for 1078 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.2656 (Rfree = 0.000) for 1076 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 14: After refmac, R = 0.2550 (Rfree = 0.000) for 1070 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.2567 (Rfree = 0.000) for 1068 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 2.57 Search for helices and strands: 0 residues in 0 chains, 1136 seeds are put forward Round 1: 106 peptides, 13 chains. Longest chain 18 peptides. Score 0.472 Round 2: 107 peptides, 10 chains. Longest chain 20 peptides. Score 0.539 Round 3: 114 peptides, 14 chains. Longest chain 15 peptides. Score 0.486 Round 4: 117 peptides, 13 chains. Longest chain 19 peptides. Score 0.520 Round 5: 108 peptides, 11 chains. Longest chain 18 peptides. Score 0.522 Taking the results from Round 2 Chains 10, Residues 97, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3699 reflections ( 99.92 % complete ) and 2146 restraints for refining 1093 atoms. 1684 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2777 (Rfree = 0.000) for 1093 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 17: After refmac, R = 0.2557 (Rfree = 0.000) for 1077 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 18: After refmac, R = 0.2484 (Rfree = 0.000) for 1078 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 19: After refmac, R = 0.2473 (Rfree = 0.000) for 1077 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2489 (Rfree = 0.000) for 1079 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 2.54 Search for helices and strands: 0 residues in 0 chains, 1130 seeds are put forward Round 1: 100 peptides, 12 chains. Longest chain 16 peptides. Score 0.466 Round 2: 106 peptides, 11 chains. Longest chain 24 peptides. Score 0.514 Round 3: 112 peptides, 14 chains. Longest chain 16 peptides. Score 0.478 Round 4: 105 peptides, 11 chains. Longest chain 20 peptides. Score 0.509 Round 5: 107 peptides, 8 chains. Longest chain 34 peptides. Score 0.579 Taking the results from Round 5 Chains 8, Residues 99, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3699 reflections ( 99.92 % complete ) and 2281 restraints for refining 1093 atoms. 1867 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2700 (Rfree = 0.000) for 1093 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2475 (Rfree = 0.000) for 1083 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 23: After refmac, R = 0.2465 (Rfree = 0.000) for 1086 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 24: After refmac, R = 0.2321 (Rfree = 0.000) for 1087 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 25: After refmac, R = 0.2272 (Rfree = 0.000) for 1087 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 2.53 Search for helices and strands: 0 residues in 0 chains, 1148 seeds are put forward Round 1: 109 peptides, 16 chains. Longest chain 12 peptides. Score 0.421 Round 2: 118 peptides, 13 chains. Longest chain 27 peptides. Score 0.524 Round 3: 104 peptides, 12 chains. Longest chain 17 peptides. Score 0.484 Round 4: 112 peptides, 8 chains. Longest chain 36 peptides. Score 0.598 Round 5: 102 peptides, 12 chains. Longest chain 15 peptides. Score 0.475 Taking the results from Round 4 Chains 8, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3699 reflections ( 99.92 % complete ) and 2304 restraints for refining 1093 atoms. 1896 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2619 (Rfree = 0.000) for 1093 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 27: After refmac, R = 0.2463 (Rfree = 0.000) for 1092 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.2325 (Rfree = 0.000) for 1093 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.2249 (Rfree = 0.000) for 1092 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2226 (Rfree = 0.000) for 1089 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 2.53 Search for helices and strands: 0 residues in 0 chains, 1139 seeds are put forward Round 1: 111 peptides, 13 chains. Longest chain 20 peptides. Score 0.494 Round 2: 117 peptides, 14 chains. Longest chain 22 peptides. Score 0.500 Round 3: 112 peptides, 12 chains. Longest chain 20 peptides. Score 0.519 Round 4: 110 peptides, 11 chains. Longest chain 22 peptides. Score 0.531 Round 5: 106 peptides, 11 chains. Longest chain 18 peptides. Score 0.514 Taking the results from Round 4 Chains 11, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3699 reflections ( 99.92 % complete ) and 2295 restraints for refining 1093 atoms. 1910 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2587 (Rfree = 0.000) for 1093 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 32: After refmac, R = 0.2363 (Rfree = 0.000) for 1089 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2299 (Rfree = 0.000) for 1088 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.2250 (Rfree = 0.000) for 1089 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2217 (Rfree = 0.000) for 1087 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 2.54 Search for helices and strands: 0 residues in 0 chains, 1128 seeds are put forward Round 1: 107 peptides, 14 chains. Longest chain 15 peptides. Score 0.455 Round 2: 112 peptides, 12 chains. Longest chain 22 peptides. Score 0.519 Round 3: 110 peptides, 11 chains. Longest chain 17 peptides. Score 0.531 Round 4: 115 peptides, 9 chains. Longest chain 26 peptides. Score 0.590 Round 5: 117 peptides, 11 chains. Longest chain 21 peptides. Score 0.559 Taking the results from Round 4 Chains 9, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3699 reflections ( 99.92 % complete ) and 2264 restraints for refining 1093 atoms. 1849 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2764 (Rfree = 0.000) for 1093 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 37: After refmac, R = 0.2551 (Rfree = 0.000) for 1085 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.2427 (Rfree = 0.000) for 1088 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.2383 (Rfree = 0.000) for 1089 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2342 (Rfree = 0.000) for 1088 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 2.55 Search for helices and strands: 0 residues in 0 chains, 1129 seeds are put forward Round 1: 105 peptides, 12 chains. Longest chain 19 peptides. Score 0.488 Round 2: 113 peptides, 11 chains. Longest chain 22 peptides. Score 0.543 Round 3: 110 peptides, 10 chains. Longest chain 19 peptides. Score 0.551 Round 4: 111 peptides, 12 chains. Longest chain 22 peptides. Score 0.515 Round 5: 104 peptides, 9 chains. Longest chain 23 peptides. Score 0.547 Taking the results from Round 3 Chains 11, Residues 100, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3699 reflections ( 99.92 % complete ) and 2218 restraints for refining 1092 atoms. 1802 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2712 (Rfree = 0.000) for 1092 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.2697 (Rfree = 0.000) for 1084 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2644 (Rfree = 0.000) for 1085 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 44: After refmac, R = 0.2747 (Rfree = 0.000) for 1080 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2606 (Rfree = 0.000) for 1082 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 2.49 Search for helices and strands: 0 residues in 0 chains, 1141 seeds are put forward Round 1: 107 peptides, 14 chains. Longest chain 13 peptides. Score 0.455 Round 2: 115 peptides, 14 chains. Longest chain 17 peptides. Score 0.491 Round 3: 109 peptides, 11 chains. Longest chain 19 peptides. Score 0.527 Round 4: 111 peptides, 12 chains. Longest chain 20 peptides. Score 0.515 Round 5: 111 peptides, 12 chains. Longest chain 23 peptides. Score 0.515 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 98, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 1vk9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3699 reflections ( 99.92 % complete ) and 2198 restraints for refining 1091 atoms. 1758 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2846 (Rfree = 0.000) for 1091 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2661 (Rfree = 0.000) for 1080 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2599 (Rfree = 0.000) for 1073 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2537 (Rfree = 0.000) for 1068 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:12 GMT 2018 Job finished. TimeTaking 31.38 Used memory is bytes: 14014848