null Sun 23 Dec 22:22:46 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 1vk9-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.4-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/1vk9-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.4-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 22:22:54 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/1vk9-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.4-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 223 and 0 Target number of residues in the AU: 223 Target solvent content: 0.6436 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: 1vk9-3.4-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: 180 Cell parameters: 132.922 132.922 66.385 90.000 90.000 120.000 Input sequence file: 1vk9-3.4-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 3.400 Wilson plot Bfac: 73.56 5103 reflections ( 99.94 % complete ) and 0 restraints for refining 1342 atoms. Observations/parameters ratio is 0.95 ------------------------------------------------------ Starting model: R = 0.3563 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3290 (Rfree = 0.000) for 1342 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 2.34 Search for helices and strands: 0 residues in 0 chains, 1367 seeds are put forward Round 1: 103 peptides, 14 chains. Longest chain 14 peptides. Score 0.436 Round 2: 121 peptides, 13 chains. Longest chain 24 peptides. Score 0.536 Round 3: 119 peptides, 12 chains. Longest chain 28 peptides. Score 0.548 Round 4: 127 peptides, 11 chains. Longest chain 30 peptides. Score 0.598 Round 5: 120 peptides, 9 chains. Longest chain 41 peptides. Score 0.609 Taking the results from Round 5 Chains 9, Residues 111, Estimated correctness of the model 31.6 % 1 chains (40 residues) have been docked in sequence ------------------------------------------------------ 5103 reflections ( 99.94 % complete ) and 2149 restraints for refining 1209 atoms. 1542 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2782 (Rfree = 0.000) for 1209 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2606 (Rfree = 0.000) for 1175 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.2540 (Rfree = 0.000) for 1164 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2514 (Rfree = 0.000) for 1161 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2420 (Rfree = 0.000) for 1157 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 2.31 Search for helices and strands: 0 residues in 0 chains, 1217 seeds are put forward Round 1: 112 peptides, 11 chains. Longest chain 27 peptides. Score 0.539 Round 2: 114 peptides, 9 chains. Longest chain 22 peptides. Score 0.586 Round 3: 120 peptides, 9 chains. Longest chain 38 peptides. Score 0.609 Round 4: 127 peptides, 9 chains. Longest chain 38 peptides. Score 0.633 Round 5: 113 peptides, 9 chains. Longest chain 19 peptides. Score 0.582 Taking the results from Round 4 Chains 10, Residues 118, Estimated correctness of the model 39.1 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5103 reflections ( 99.94 % complete ) and 2137 restraints for refining 1097 atoms. 1645 conditional restraints added. Observations/parameters ratio is 1.16 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2714 (Rfree = 0.000) for 1097 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 7: After refmac, R = 0.2498 (Rfree = 0.000) for 1098 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 8: After refmac, R = 0.2445 (Rfree = 0.000) for 1099 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.2332 (Rfree = 0.000) for 1101 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.2281 (Rfree = 0.000) for 1100 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 2.34 Search for helices and strands: 0 residues in 0 chains, 1144 seeds are put forward Round 1: 111 peptides, 11 chains. Longest chain 21 peptides. Score 0.535 Round 2: 123 peptides, 9 chains. Longest chain 36 peptides. Score 0.619 Round 3: 122 peptides, 9 chains. Longest chain 36 peptides. Score 0.616 Round 4: 125 peptides, 9 chains. Longest chain 40 peptides. Score 0.626 Round 5: 127 peptides, 10 chains. Longest chain 35 peptides. Score 0.616 Taking the results from Round 4 Chains 9, Residues 116, Estimated correctness of the model 36.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5103 reflections ( 99.94 % complete ) and 2175 restraints for refining 1098 atoms. 1720 conditional restraints added. Observations/parameters ratio is 1.16 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2558 (Rfree = 0.000) for 1098 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 12: After refmac, R = 0.2432 (Rfree = 0.000) for 1099 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.2380 (Rfree = 0.000) for 1101 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2337 (Rfree = 0.000) for 1103 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2292 (Rfree = 0.000) for 1103 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 2.30 Search for helices and strands: 0 residues in 0 chains, 1154 seeds are put forward Round 1: 124 peptides, 11 chains. Longest chain 25 peptides. Score 0.586 Round 2: 128 peptides, 10 chains. Longest chain 30 peptides. Score 0.619 Round 3: 128 peptides, 10 chains. Longest chain 29 peptides. Score 0.619 Round 4: 125 peptides, 12 chains. Longest chain 19 peptides. Score 0.572 Round 5: 126 peptides, 10 chains. Longest chain 49 peptides. Score 0.612 Taking the results from Round 3 Chains 10, Residues 118, Estimated correctness of the model 34.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5103 reflections ( 99.94 % complete ) and 2253 restraints for refining 1098 atoms. 1791 conditional restraints added. Observations/parameters ratio is 1.16 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2592 (Rfree = 0.000) for 1098 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 17: After refmac, R = 0.2373 (Rfree = 0.000) for 1099 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.2356 (Rfree = 0.000) for 1102 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2314 (Rfree = 0.000) for 1104 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2313 (Rfree = 0.000) for 1103 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 2.28 Search for helices and strands: 0 residues in 0 chains, 1150 seeds are put forward Round 1: 123 peptides, 12 chains. Longest chain 20 peptides. Score 0.564 Round 2: 124 peptides, 12 chains. Longest chain 26 peptides. Score 0.568 Round 3: 120 peptides, 11 chains. Longest chain 21 peptides. Score 0.571 Round 4: 124 peptides, 10 chains. Longest chain 28 peptides. Score 0.605 Round 5: 126 peptides, 9 chains. Longest chain 29 peptides. Score 0.630 Taking the results from Round 5 Chains 10, Residues 117, Estimated correctness of the model 38.2 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 5103 reflections ( 99.94 % complete ) and 2091 restraints for refining 1164 atoms. 1462 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2956 (Rfree = 0.000) for 1164 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 22: After refmac, R = 0.2411 (Rfree = 0.000) for 1145 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2386 (Rfree = 0.000) for 1145 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2272 (Rfree = 0.000) for 1149 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2165 (Rfree = 0.000) for 1150 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.28 Search for helices and strands: 0 residues in 0 chains, 1203 seeds are put forward Round 1: 133 peptides, 11 chains. Longest chain 33 peptides. Score 0.619 Round 2: 133 peptides, 13 chains. Longest chain 19 peptides. Score 0.584 Round 3: 137 peptides, 8 chains. Longest chain 28 peptides. Score 0.683 Round 4: 129 peptides, 9 chains. Longest chain 42 peptides. Score 0.640 Round 5: 135 peptides, 8 chains. Longest chain 40 peptides. Score 0.677 Taking the results from Round 3 Chains 10, Residues 129, Estimated correctness of the model 53.4 % 3 chains (68 residues) have been docked in sequence ------------------------------------------------------ 5103 reflections ( 99.94 % complete ) and 1847 restraints for refining 1212 atoms. 1048 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2722 (Rfree = 0.000) for 1212 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 27: After refmac, R = 0.2531 (Rfree = 0.000) for 1199 atoms. Found 8 (9 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.2788 (Rfree = 0.000) for 1192 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.2401 (Rfree = 0.000) for 1186 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.2577 (Rfree = 0.000) for 1184 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 2.28 Search for helices and strands: 0 residues in 0 chains, 1215 seeds are put forward Round 1: 127 peptides, 12 chains. Longest chain 32 peptides. Score 0.579 Round 2: 135 peptides, 10 chains. Longest chain 29 peptides. Score 0.643 Round 3: 130 peptides, 9 chains. Longest chain 40 peptides. Score 0.644 Round 4: 127 peptides, 10 chains. Longest chain 25 peptides. Score 0.616 Round 5: 123 peptides, 11 chains. Longest chain 33 peptides. Score 0.583 Taking the results from Round 3 Chains 9, Residues 121, Estimated correctness of the model 42.4 % 1 chains (39 residues) have been docked in sequence ------------------------------------------------------ 5103 reflections ( 99.94 % complete ) and 2003 restraints for refining 1138 atoms. 1373 conditional restraints added. Observations/parameters ratio is 1.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2557 (Rfree = 0.000) for 1138 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 32: After refmac, R = 0.2393 (Rfree = 0.000) for 1131 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 33: After refmac, R = 0.2251 (Rfree = 0.000) for 1129 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2207 (Rfree = 0.000) for 1131 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2193 (Rfree = 0.000) for 1133 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 2.30 Search for helices and strands: 0 residues in 0 chains, 1162 seeds are put forward Round 1: 125 peptides, 13 chains. Longest chain 18 peptides. Score 0.553 Round 2: 128 peptides, 12 chains. Longest chain 23 peptides. Score 0.583 Round 3: 125 peptides, 9 chains. Longest chain 23 peptides. Score 0.626 Round 4: 124 peptides, 9 chains. Longest chain 26 peptides. Score 0.623 Round 5: 119 peptides, 11 chains. Longest chain 25 peptides. Score 0.567 Taking the results from Round 3 Chains 10, Residues 116, Estimated correctness of the model 36.9 % 3 chains (49 residues) have been docked in sequence ------------------------------------------------------ 5103 reflections ( 99.94 % complete ) and 1880 restraints for refining 1144 atoms. 1235 conditional restraints added. Observations/parameters ratio is 1.12 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2728 (Rfree = 0.000) for 1144 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 37: After refmac, R = 0.2373 (Rfree = 0.000) for 1127 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 38: After refmac, R = 0.2268 (Rfree = 0.000) for 1123 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.2396 (Rfree = 0.000) for 1124 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.2095 (Rfree = 0.000) for 1120 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 2.28 Search for helices and strands: 0 residues in 0 chains, 1162 seeds are put forward Round 1: 111 peptides, 12 chains. Longest chain 23 peptides. Score 0.515 Round 2: 125 peptides, 12 chains. Longest chain 17 peptides. Score 0.572 Round 3: 127 peptides, 10 chains. Longest chain 46 peptides. Score 0.616 Round 4: 129 peptides, 10 chains. Longest chain 34 peptides. Score 0.623 Round 5: 128 peptides, 10 chains. Longest chain 33 peptides. Score 0.619 Taking the results from Round 4 Chains 10, Residues 119, Estimated correctness of the model 36.0 % 1 chains (33 residues) have been docked in sequence ------------------------------------------------------ 5103 reflections ( 99.94 % complete ) and 1996 restraints for refining 1136 atoms. 1401 conditional restraints added. Observations/parameters ratio is 1.12 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2891 (Rfree = 0.000) for 1136 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 42: After refmac, R = 0.2761 (Rfree = 0.000) for 1130 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 43: After refmac, R = 0.2460 (Rfree = 0.000) for 1123 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.2523 (Rfree = 0.000) for 1122 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 45: After refmac, R = 0.2428 (Rfree = 0.000) for 1120 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.27 Search for helices and strands: 0 residues in 0 chains, 1161 seeds are put forward Round 1: 117 peptides, 12 chains. Longest chain 21 peptides. Score 0.540 Round 2: 131 peptides, 8 chains. Longest chain 44 peptides. Score 0.664 Round 3: 120 peptides, 9 chains. Longest chain 34 peptides. Score 0.609 Round 4: 122 peptides, 10 chains. Longest chain 25 peptides. Score 0.598 Round 5: 114 peptides, 9 chains. Longest chain 29 peptides. Score 0.586 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 123, Estimated correctness of the model 48.2 % 2 chains (60 residues) have been docked in sequence Sequence coverage is 48 % Consider running further cycles of model building using 1vk9-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 94 A and 100 A 8 chains (128 residues) following loop building 1 chains (65 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5103 reflections ( 99.94 % complete ) and 1620 restraints for refining 1148 atoms. 845 conditional restraints added. Observations/parameters ratio is 1.11 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2878 (Rfree = 0.000) for 1148 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2821 (Rfree = 0.000) for 1142 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2608 (Rfree = 0.000) for 1137 atoms. Found 0 (8 requested) and removed 2 (4 requested) atoms. Cycle 49: After refmac, R = 0.2557 (Rfree = 0.000) for 1135 atoms. Found 0 (8 requested) and removed 0 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:55:53 GMT 2018 Job finished. TimeTaking 33.11 Used memory is bytes: 170608