null Sun 23 Dec 22:23:01 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 1vjf-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-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/1vjf-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-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 22:23:10 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/1vjf-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.5217 Checking the provided sequence file Detected sequence length: 180 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 180 Adjusted target solvent content: 0.38 Input MTZ file: 1vjf-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: 96 Cell parameters: 50.903 50.903 121.411 90.000 90.000 90.000 Input sequence file: 1vjf-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1440 target number of atoms Had to go as low as 0.55 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: 46.944 3.200 Wilson plot Bfac: 27.90 2942 reflections ( 99.80 % complete ) and 0 restraints for refining 1597 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3080 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2542 (Rfree = 0.000) for 1597 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.72 3.20 Search for helices and strands: 0 residues in 0 chains, 1633 seeds are put forward Round 1: 90 peptides, 17 chains. Longest chain 14 peptides. Score 0.402 Round 2: 105 peptides, 16 chains. Longest chain 13 peptides. Score 0.571 Round 3: 122 peptides, 14 chains. Longest chain 25 peptides. Score 0.736 Round 4: 117 peptides, 14 chains. Longest chain 14 peptides. Score 0.709 Round 5: 123 peptides, 12 chains. Longest chain 34 peptides. Score 0.784 Taking the results from Round 5 Chains 12, Residues 111, Estimated correctness of the model 80.9 % 2 chains (52 residues) have been docked in sequence Building loops using Loopy2018 12 chains (111 residues) following loop building 2 chains (52 residues) in sequence following loop building ------------------------------------------------------ 2942 reflections ( 99.80 % complete ) and 2273 restraints for refining 1313 atoms. 1629 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2722 (Rfree = 0.000) for 1313 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 2: After refmac, R = 0.2657 (Rfree = 0.000) for 1290 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.2478 (Rfree = 0.000) for 1281 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2323 (Rfree = 0.000) for 1273 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2222 (Rfree = 0.000) for 1267 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.68 3.15 Search for helices and strands: 0 residues in 0 chains, 1316 seeds are put forward Round 1: 110 peptides, 15 chains. Longest chain 26 peptides. Score 0.639 Round 2: 120 peptides, 13 chains. Longest chain 26 peptides. Score 0.749 Round 3: 113 peptides, 12 chains. Longest chain 27 peptides. Score 0.737 Round 4: 120 peptides, 11 chains. Longest chain 25 peptides. Score 0.791 Round 5: 117 peptides, 11 chains. Longest chain 33 peptides. Score 0.778 Taking the results from Round 4 Chains 12, Residues 109, Estimated correctness of the model 82.0 % 3 chains (40 residues) have been docked in sequence Building loops using Loopy2018 12 chains (109 residues) following loop building 3 chains (40 residues) in sequence following loop building ------------------------------------------------------ 2942 reflections ( 99.80 % complete ) and 2524 restraints for refining 1307 atoms. 1941 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2978 (Rfree = 0.000) for 1307 atoms. Found 7 (10 requested) and removed 18 (5 requested) atoms. Cycle 7: After refmac, R = 0.2523 (Rfree = 0.000) for 1283 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2402 (Rfree = 0.000) for 1269 atoms. Found 4 (9 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2445 (Rfree = 0.000) for 1264 atoms. Found 9 (9 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.2313 (Rfree = 0.000) for 1262 atoms. Found 7 (9 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.68 3.15 Search for helices and strands: 0 residues in 0 chains, 1309 seeds are put forward Round 1: 114 peptides, 15 chains. Longest chain 26 peptides. Score 0.665 Round 2: 118 peptides, 13 chains. Longest chain 26 peptides. Score 0.739 Round 3: 129 peptides, 10 chains. Longest chain 28 peptides. Score 0.841 Round 4: 120 peptides, 15 chains. Longest chain 22 peptides. Score 0.701 Round 5: 122 peptides, 11 chains. Longest chain 30 peptides. Score 0.799 Taking the results from Round 3 Chains 12, Residues 119, Estimated correctness of the model 89.1 % 4 chains (65 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 68 A 10 chains (122 residues) following loop building 3 chains (70 residues) in sequence following loop building ------------------------------------------------------ 2942 reflections ( 99.80 % complete ) and 2137 restraints for refining 1314 atoms. 1418 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2806 (Rfree = 0.000) for 1314 atoms. Found 6 (9 requested) and removed 19 (5 requested) atoms. Cycle 12: After refmac, R = 0.2548 (Rfree = 0.000) for 1291 atoms. Found 9 (9 requested) and removed 12 (5 requested) atoms. Cycle 13: After refmac, R = 0.2399 (Rfree = 0.000) for 1283 atoms. Found 3 (8 requested) and removed 12 (5 requested) atoms. Cycle 14: After refmac, R = 0.2419 (Rfree = 0.000) for 1273 atoms. Found 4 (8 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2435 (Rfree = 0.000) for 1268 atoms. Found 6 (8 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.65 3.12 Search for helices and strands: 0 residues in 0 chains, 1321 seeds are put forward Round 1: 109 peptides, 16 chains. Longest chain 19 peptides. Score 0.601 Round 2: 115 peptides, 14 chains. Longest chain 15 peptides. Score 0.698 Round 3: 127 peptides, 14 chains. Longest chain 21 peptides. Score 0.760 Round 4: 127 peptides, 12 chains. Longest chain 27 peptides. Score 0.800 Round 5: 123 peptides, 14 chains. Longest chain 15 peptides. Score 0.741 Taking the results from Round 4 Chains 12, Residues 115, Estimated correctness of the model 83.4 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 2942 reflections ( 99.80 % complete ) and 2612 restraints for refining 1313 atoms. 2061 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2612 (Rfree = 0.000) for 1313 atoms. Found 7 (8 requested) and removed 11 (5 requested) atoms. Cycle 17: After refmac, R = 0.2401 (Rfree = 0.000) for 1305 atoms. Found 6 (7 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.2313 (Rfree = 0.000) for 1305 atoms. Found 2 (7 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2278 (Rfree = 0.000) for 1299 atoms. Found 3 (7 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2617 (Rfree = 0.000) for 1296 atoms. Found 7 (7 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.64 3.11 Search for helices and strands: 0 residues in 0 chains, 1328 seeds are put forward Round 1: 103 peptides, 14 chains. Longest chain 26 peptides. Score 0.621 Round 2: 106 peptides, 15 chains. Longest chain 14 peptides. Score 0.611 Round 3: 107 peptides, 14 chains. Longest chain 27 peptides. Score 0.648 Round 4: 106 peptides, 15 chains. Longest chain 15 peptides. Score 0.611 Round 5: 113 peptides, 14 chains. Longest chain 24 peptides. Score 0.686 Taking the results from Round 5 Chains 14, Residues 99, Estimated correctness of the model 62.2 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 2942 reflections ( 99.80 % complete ) and 2679 restraints for refining 1314 atoms. 2212 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2576 (Rfree = 0.000) for 1314 atoms. Found 7 (7 requested) and removed 11 (5 requested) atoms. Cycle 22: After refmac, R = 0.2321 (Rfree = 0.000) for 1298 atoms. Found 2 (7 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.2299 (Rfree = 0.000) for 1287 atoms. Found 7 (7 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2249 (Rfree = 0.000) for 1287 atoms. Found 7 (7 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2182 (Rfree = 0.000) for 1288 atoms. Found 1 (7 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.66 3.13 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward Round 1: 90 peptides, 13 chains. Longest chain 24 peptides. Score 0.556 Round 2: 93 peptides, 14 chains. Longest chain 13 peptides. Score 0.545 Round 3: 97 peptides, 12 chains. Longest chain 27 peptides. Score 0.641 Round 4: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.517 Round 5: 105 peptides, 15 chains. Longest chain 27 peptides. Score 0.604 Taking the results from Round 3 Chains 13, Residues 85, Estimated correctness of the model 51.6 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 2942 reflections ( 99.80 % complete ) and 2756 restraints for refining 1313 atoms. 2329 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2435 (Rfree = 0.000) for 1313 atoms. Found 5 (7 requested) and removed 11 (5 requested) atoms. Cycle 27: After refmac, R = 0.2388 (Rfree = 0.000) for 1307 atoms. Found 7 (7 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.2277 (Rfree = 0.000) for 1306 atoms. Found 4 (7 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2192 (Rfree = 0.000) for 1302 atoms. Found 3 (7 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2175 (Rfree = 0.000) for 1300 atoms. Found 1 (7 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.68 3.15 Search for helices and strands: 0 residues in 0 chains, 1334 seeds are put forward Round 1: 91 peptides, 13 chains. Longest chain 27 peptides. Score 0.564 Round 2: 99 peptides, 13 chains. Longest chain 27 peptides. Score 0.624 Round 3: 98 peptides, 14 chains. Longest chain 13 peptides. Score 0.584 Round 4: 96 peptides, 13 chains. Longest chain 16 peptides. Score 0.602 Round 5: 99 peptides, 12 chains. Longest chain 27 peptides. Score 0.655 Taking the results from Round 5 Chains 12, Residues 87, Estimated correctness of the model 55.0 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 2942 reflections ( 99.80 % complete ) and 2724 restraints for refining 1314 atoms. 2285 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2614 (Rfree = 0.000) for 1314 atoms. Found 7 (7 requested) and removed 12 (5 requested) atoms. Cycle 32: After refmac, R = 0.2683 (Rfree = 0.000) for 1306 atoms. Found 7 (7 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.2548 (Rfree = 0.000) for 1301 atoms. Found 2 (7 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2316 (Rfree = 0.000) for 1296 atoms. Found 3 (7 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2205 (Rfree = 0.000) for 1294 atoms. Found 2 (7 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.62 3.08 Search for helices and strands: 0 residues in 0 chains, 1328 seeds are put forward Round 1: 96 peptides, 14 chains. Longest chain 20 peptides. Score 0.569 Round 2: 104 peptides, 13 chains. Longest chain 27 peptides. Score 0.658 Round 3: 105 peptides, 13 chains. Longest chain 18 peptides. Score 0.665 Round 4: 99 peptides, 13 chains. Longest chain 16 peptides. Score 0.624 Round 5: 96 peptides, 15 chains. Longest chain 13 peptides. Score 0.534 Taking the results from Round 3 Chains 13, Residues 92, Estimated correctness of the model 57.4 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 2942 reflections ( 99.80 % complete ) and 2736 restraints for refining 1314 atoms. 2310 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2280 (Rfree = 0.000) for 1314 atoms. Found 5 (7 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.2129 (Rfree = 0.000) for 1311 atoms. Found 5 (7 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.2005 (Rfree = 0.000) for 1308 atoms. Found 3 (7 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1967 (Rfree = 0.000) for 1306 atoms. Found 3 (7 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1929 (Rfree = 0.000) for 1304 atoms. Found 2 (7 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.70 3.18 Search for helices and strands: 0 residues in 0 chains, 1342 seeds are put forward Round 1: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.487 Round 2: 84 peptides, 12 chains. Longest chain 19 peptides. Score 0.543 Round 3: 93 peptides, 11 chains. Longest chain 27 peptides. Score 0.645 Round 4: 91 peptides, 11 chains. Longest chain 27 peptides. Score 0.631 Round 5: 85 peptides, 10 chains. Longest chain 27 peptides. Score 0.621 Taking the results from Round 3 Chains 11, Residues 82, Estimated correctness of the model 52.6 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 2942 reflections ( 99.80 % complete ) and 2722 restraints for refining 1314 atoms. 2302 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2212 (Rfree = 0.000) for 1314 atoms. Found 5 (7 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.2113 (Rfree = 0.000) for 1313 atoms. Found 6 (7 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2054 (Rfree = 0.000) for 1309 atoms. Found 3 (7 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2043 (Rfree = 0.000) for 1306 atoms. Found 2 (7 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1995 (Rfree = 0.000) for 1303 atoms. Found 4 (7 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.66 3.13 Search for helices and strands: 0 residues in 0 chains, 1338 seeds are put forward Round 1: 78 peptides, 10 chains. Longest chain 19 peptides. Score 0.567 Round 2: 84 peptides, 9 chains. Longest chain 19 peptides. Score 0.646 Round 3: 74 peptides, 9 chains. Longest chain 13 peptides. Score 0.571 Round 4: 80 peptides, 9 chains. Longest chain 24 peptides. Score 0.618 Round 5: 78 peptides, 12 chains. Longest chain 13 peptides. Score 0.490 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 75, Estimated correctness of the model 52.9 % 1 chains (17 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 1vjf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2942 reflections ( 99.80 % complete ) and 2805 restraints for refining 1308 atoms. 2452 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2077 (Rfree = 0.000) for 1308 atoms. Found 0 (7 requested) and removed 3 (5 requested) atoms. Cycle 47: After refmac, R = 0.2094 (Rfree = 0.000) for 1303 atoms. Found 0 (7 requested) and removed 2 (5 requested) atoms. Cycle 48: After refmac, R = 0.1903 (Rfree = 0.000) for 1300 atoms. Found 0 (7 requested) and removed 4 (5 requested) atoms. Cycle 49: After refmac, R = 0.1951 (Rfree = 0.000) for 1296 atoms. Found 0 (7 requested) and removed 4 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:20 GMT 2018 Job finished. TimeTaking 28.32 Used memory is bytes: 22198200