Sun 23 Dec 23:49:21 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fqp-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-parrot-mrncs ############### 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 23:49:25 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-parrot-mrncs/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 222 and 0 Target number of residues in the AU: 222 Target solvent content: 0.6452 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-4.0-parrot-mrncs.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: 4 Cell parameters: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3104 target number of atoms Had to go as low as 0.60 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 50.895 4.000 Wilson plot Bfac: 74.98 2328 reflections ( 81.71 % complete ) and 0 restraints for refining 3432 atoms. Observations/parameters ratio is 0.17 ------------------------------------------------------ Starting model: R = 0.3201 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2928 (Rfree = 0.000) for 3432 atoms. Found 16 (16 requested) and removed 67 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 4.12 Search for helices and strands: 0 residues in 0 chains, 3427 seeds are put forward NCS extension: 0 residues added, 3427 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 7 peptides. Score 0.225 Round 2: 103 peptides, 20 chains. Longest chain 12 peptides. Score 0.301 Round 3: 109 peptides, 20 chains. Longest chain 14 peptides. Score 0.332 Round 4: 111 peptides, 20 chains. Longest chain 15 peptides. Score 0.343 Round 5: 114 peptides, 20 chains. Longest chain 11 peptides. Score 0.358 Taking the results from Round 5 Chains 20, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 7028 restraints for refining 2802 atoms. 6672 conditional restraints added. Observations/parameters ratio is 0.21 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2051 (Rfree = 0.000) for 2802 atoms. Found 9 (13 requested) and removed 23 (6 requested) atoms. Cycle 2: After refmac, R = 0.1891 (Rfree = 0.000) for 2755 atoms. Found 10 (13 requested) and removed 21 (6 requested) atoms. Cycle 3: After refmac, R = 0.1505 (Rfree = 0.000) for 2717 atoms. Found 2 (13 requested) and removed 12 (6 requested) atoms. Cycle 4: After refmac, R = 0.1438 (Rfree = 0.000) for 2692 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.1317 (Rfree = 0.000) for 2682 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 4.12 Search for helices and strands: 0 residues in 0 chains, 2741 seeds are put forward NCS extension: 0 residues added, 2741 seeds are put forward Round 1: 96 peptides, 22 chains. Longest chain 6 peptides. Score 0.214 Round 2: 132 peptides, 26 chains. Longest chain 9 peptides. Score 0.319 Round 3: 121 peptides, 21 chains. Longest chain 13 peptides. Score 0.371 Round 4: 120 peptides, 21 chains. Longest chain 10 peptides. Score 0.366 Round 5: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.373 Taking the results from Round 5 Chains 20, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5863 restraints for refining 2477 atoms. 5495 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1473 (Rfree = 0.000) for 2477 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 7: After refmac, R = 0.1281 (Rfree = 0.000) for 2463 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.1143 (Rfree = 0.000) for 2456 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.1080 (Rfree = 0.000) for 2449 atoms. Found 0 (11 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.1023 (Rfree = 0.000) for 2440 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 4.20 Search for helices and strands: 0 residues in 0 chains, 2501 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2504 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 7 peptides. Score 0.292 Round 2: 152 peptides, 26 chains. Longest chain 10 peptides. Score 0.416 Round 3: 148 peptides, 23 chains. Longest chain 17 peptides. Score 0.457 Round 4: 145 peptides, 22 chains. Longest chain 19 peptides. Score 0.463 Round 5: 140 peptides, 22 chains. Longest chain 18 peptides. Score 0.441 Taking the results from Round 4 Chains 22, Residues 123, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5623 restraints for refining 2496 atoms. 5132 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1764 (Rfree = 0.000) for 2496 atoms. Found 11 (11 requested) and removed 31 (5 requested) atoms. Cycle 12: After refmac, R = 0.1268 (Rfree = 0.000) for 2466 atoms. Found 8 (11 requested) and removed 22 (5 requested) atoms. Cycle 13: After refmac, R = 0.1226 (Rfree = 0.000) for 2446 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.1194 (Rfree = 0.000) for 2442 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. Cycle 15: After refmac, R = 0.1222 (Rfree = 0.000) for 2430 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 4.17 Search for helices and strands: 0 residues in 0 chains, 2489 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 2521 seeds are put forward Round 1: 101 peptides, 22 chains. Longest chain 6 peptides. Score 0.243 Round 2: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.345 Round 3: 123 peptides, 22 chains. Longest chain 9 peptides. Score 0.360 Round 4: 131 peptides, 23 chains. Longest chain 11 peptides. Score 0.378 Round 5: 129 peptides, 21 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 5 Chains 21, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5959 restraints for refining 2504 atoms. 5548 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1467 (Rfree = 0.000) for 2504 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 17: After refmac, R = 0.1389 (Rfree = 0.000) for 2481 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 18: After refmac, R = 0.1179 (Rfree = 0.000) for 2471 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.1224 (Rfree = 0.000) for 2461 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.1270 (Rfree = 0.000) for 2459 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 4.18 Search for helices and strands: 0 residues in 0 chains, 2520 seeds are put forward NCS extension: 0 residues added, 2520 seeds are put forward Round 1: 119 peptides, 24 chains. Longest chain 8 peptides. Score 0.296 Round 2: 135 peptides, 25 chains. Longest chain 11 peptides. Score 0.356 Round 3: 128 peptides, 23 chains. Longest chain 14 peptides. Score 0.363 Round 4: 142 peptides, 24 chains. Longest chain 12 peptides. Score 0.410 Round 5: 151 peptides, 23 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 5 Chains 23, Residues 128, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5874 restraints for refining 2566 atoms. 5356 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1527 (Rfree = 0.000) for 2566 atoms. Found 11 (12 requested) and removed 40 (6 requested) atoms. Cycle 22: After refmac, R = 0.1358 (Rfree = 0.000) for 2525 atoms. Found 7 (12 requested) and removed 19 (6 requested) atoms. Cycle 23: After refmac, R = 0.1272 (Rfree = 0.000) for 2508 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1183 (Rfree = 0.000) for 2506 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1195 (Rfree = 0.000) for 2498 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 4.26 Search for helices and strands: 0 residues in 0 chains, 2571 seeds are put forward NCS extension: 0 residues added, 2571 seeds are put forward Round 1: 121 peptides, 27 chains. Longest chain 7 peptides. Score 0.239 Round 2: 145 peptides, 28 chains. Longest chain 9 peptides. Score 0.342 Round 3: 146 peptides, 27 chains. Longest chain 9 peptides. Score 0.368 Round 4: 147 peptides, 26 chains. Longest chain 10 peptides. Score 0.393 Round 5: 137 peptides, 22 chains. Longest chain 12 peptides. Score 0.427 Taking the results from Round 5 Chains 22, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 6044 restraints for refining 2561 atoms. 5606 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1514 (Rfree = 0.000) for 2561 atoms. Found 8 (12 requested) and removed 18 (6 requested) atoms. Cycle 27: After refmac, R = 0.1419 (Rfree = 0.000) for 2538 atoms. Found 4 (12 requested) and removed 15 (6 requested) atoms. Cycle 28: After refmac, R = 0.1200 (Rfree = 0.000) for 2526 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1114 (Rfree = 0.000) for 2524 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1163 (Rfree = 0.000) for 2517 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 4.23 Search for helices and strands: 0 residues in 0 chains, 2582 seeds are put forward NCS extension: 0 residues added, 2582 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 8 peptides. Score 0.238 Round 2: 122 peptides, 25 chains. Longest chain 7 peptides. Score 0.289 Round 3: 127 peptides, 25 chains. Longest chain 8 peptides. Score 0.315 Round 4: 129 peptides, 24 chains. Longest chain 12 peptides. Score 0.347 Round 5: 131 peptides, 23 chains. Longest chain 10 peptides. Score 0.378 Taking the results from Round 5 Chains 23, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 6270 restraints for refining 2579 atoms. 5861 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1458 (Rfree = 0.000) for 2579 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 32: After refmac, R = 0.1528 (Rfree = 0.000) for 2563 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.1287 (Rfree = 0.000) for 2560 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.1299 (Rfree = 0.000) for 2556 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1189 (Rfree = 0.000) for 2549 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 4.27 Search for helices and strands: 0 residues in 0 chains, 2594 seeds are put forward NCS extension: 0 residues added, 2594 seeds are put forward Round 1: 94 peptides, 21 chains. Longest chain 7 peptides. Score 0.227 Round 2: 111 peptides, 21 chains. Longest chain 11 peptides. Score 0.320 Round 3: 116 peptides, 23 chains. Longest chain 10 peptides. Score 0.302 Round 4: 125 peptides, 22 chains. Longest chain 13 peptides. Score 0.370 Round 5: 120 peptides, 21 chains. Longest chain 17 peptides. Score 0.366 Taking the results from Round 4 Chains 22, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 6130 restraints for refining 2560 atoms. 5740 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1542 (Rfree = 0.000) for 2560 atoms. Found 10 (12 requested) and removed 16 (6 requested) atoms. Cycle 37: After refmac, R = 0.1415 (Rfree = 0.000) for 2546 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.1185 (Rfree = 0.000) for 2536 atoms. Found 1 (12 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1167 (Rfree = 0.000) for 2523 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.1153 (Rfree = 0.000) for 2515 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 4.23 Search for helices and strands: 0 residues in 0 chains, 2552 seeds are put forward NCS extension: 0 residues added, 2552 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.254 Round 2: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.290 Round 3: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.289 Round 4: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.291 Round 5: 106 peptides, 18 chains. Longest chain 9 peptides. Score 0.362 Taking the results from Round 5 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 6233 restraints for refining 2555 atoms. 5899 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1314 (Rfree = 0.000) for 2555 atoms. Found 8 (12 requested) and removed 15 (6 requested) atoms. Cycle 42: After refmac, R = 0.1213 (Rfree = 0.000) for 2537 atoms. Found 5 (12 requested) and removed 12 (6 requested) atoms. Cycle 43: After refmac, R = 0.1245 (Rfree = 0.000) for 2525 atoms. Found 9 (12 requested) and removed 14 (6 requested) atoms. Cycle 44: After refmac, R = 0.0996 (Rfree = 0.000) for 2517 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.1133 (Rfree = 0.000) for 2513 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 4.24 Search for helices and strands: 0 residues in 0 chains, 2561 seeds are put forward NCS extension: 0 residues added, 2561 seeds are put forward Round 1: 80 peptides, 19 chains. Longest chain 5 peptides. Score 0.192 Round 2: 88 peptides, 20 chains. Longest chain 6 peptides. Score 0.216 Round 3: 84 peptides, 17 chains. Longest chain 7 peptides. Score 0.266 Round 4: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.282 Round 5: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.311 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 75, 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 2fqp-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2328 reflections ( 81.71 % complete ) and 6289 restraints for refining 2516 atoms. 6006 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1252 (Rfree = 0.000) for 2516 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1575 (Rfree = 0.000) for 2509 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1113 (Rfree = 0.000) for 2504 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1307 (Rfree = 0.000) for 2497 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 30.33