null Sun 23 Dec 22:22:59 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 2obp-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obp-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obp-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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/2obp-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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 22:23:08 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/2obp-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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 162 and 0 Target number of residues in the AU: 162 Target solvent content: 0.6260 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.56 Input MTZ file: 2obp-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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.70 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: 29.462 3.200 Wilson plot Bfac: 63.74 4340 reflections ( 99.47 % complete ) and 0 restraints for refining 1708 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Starting model: R = 0.3560 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3347 (Rfree = 0.000) for 1708 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.04 Search for helices and strands: 0 residues in 0 chains, 1747 seeds are put forward NCS extension: 0 residues added, 1747 seeds are put forward Round 1: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.339 Round 2: 104 peptides, 14 chains. Longest chain 14 peptides. Score 0.520 Round 3: 107 peptides, 15 chains. Longest chain 12 peptides. Score 0.511 Round 4: 118 peptides, 14 chains. Longest chain 16 peptides. Score 0.597 Round 5: 121 peptides, 13 chains. Longest chain 17 peptides. Score 0.635 Taking the results from Round 5 Chains 14, Residues 108, Estimated correctness of the model 50.2 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2799 restraints for refining 1387 atoms. 2326 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3108 (Rfree = 0.000) for 1387 atoms. Found 7 (12 requested) and removed 15 (6 requested) atoms. Cycle 2: After refmac, R = 0.3069 (Rfree = 0.000) for 1348 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.3012 (Rfree = 0.000) for 1323 atoms. Found 8 (12 requested) and removed 11 (6 requested) atoms. Cycle 4: After refmac, R = 0.2909 (Rfree = 0.000) for 1312 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.2840 (Rfree = 0.000) for 1302 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 1349 seeds are put forward NCS extension: 0 residues added, 1349 seeds are put forward Round 1: 97 peptides, 16 chains. Longest chain 12 peptides. Score 0.419 Round 2: 99 peptides, 14 chains. Longest chain 11 peptides. Score 0.489 Round 3: 110 peptides, 15 chains. Longest chain 14 peptides. Score 0.528 Round 4: 112 peptides, 16 chains. Longest chain 12 peptides. Score 0.514 Round 5: 106 peptides, 14 chains. Longest chain 15 peptides. Score 0.531 Taking the results from Round 5 Chains 14, Residues 92, Estimated correctness of the model 21.1 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2880 restraints for refining 1329 atoms. 2505 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2839 (Rfree = 0.000) for 1329 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 7: After refmac, R = 0.2806 (Rfree = 0.000) for 1320 atoms. Found 9 (11 requested) and removed 12 (5 requested) atoms. Cycle 8: After refmac, R = 0.2827 (Rfree = 0.000) for 1312 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 9: After refmac, R = 0.2808 (Rfree = 0.000) for 1304 atoms. Found 6 (11 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.2739 (Rfree = 0.000) for 1294 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 2.88 Search for helices and strands: 0 residues in 0 chains, 1345 seeds are put forward NCS extension: 0 residues added, 1345 seeds are put forward Round 1: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.439 Round 2: 111 peptides, 13 chains. Longest chain 19 peptides. Score 0.585 Round 3: 122 peptides, 14 chains. Longest chain 20 peptides. Score 0.618 Round 4: 120 peptides, 14 chains. Longest chain 21 peptides. Score 0.607 Round 5: 124 peptides, 14 chains. Longest chain 19 peptides. Score 0.627 Taking the results from Round 5 Chains 14, Residues 110, Estimated correctness of the model 48.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2793 restraints for refining 1315 atoms. 2367 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3067 (Rfree = 0.000) for 1315 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 12: After refmac, R = 0.2887 (Rfree = 0.000) for 1306 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 13: After refmac, R = 0.2733 (Rfree = 0.000) for 1298 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.2536 (Rfree = 0.000) for 1295 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2597 (Rfree = 0.000) for 1289 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.16 Search for helices and strands: 0 residues in 0 chains, 1357 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1373 seeds are put forward Round 1: 112 peptides, 17 chains. Longest chain 14 peptides. Score 0.488 Round 2: 112 peptides, 14 chains. Longest chain 19 peptides. Score 0.565 Round 3: 126 peptides, 15 chains. Longest chain 16 peptides. Score 0.615 Round 4: 117 peptides, 13 chains. Longest chain 18 peptides. Score 0.616 Round 5: 121 peptides, 15 chains. Longest chain 17 peptides. Score 0.589 Taking the results from Round 4 Chains 13, Residues 104, Estimated correctness of the model 45.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2943 restraints for refining 1340 atoms. 2540 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2975 (Rfree = 0.000) for 1340 atoms. Found 11 (12 requested) and removed 12 (6 requested) atoms. Cycle 17: After refmac, R = 0.2858 (Rfree = 0.000) for 1329 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. Cycle 18: After refmac, R = 0.2789 (Rfree = 0.000) for 1319 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2767 (Rfree = 0.000) for 1318 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.2800 (Rfree = 0.000) for 1313 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 2.84 Search for helices and strands: 0 residues in 0 chains, 1376 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1396 seeds are put forward Round 1: 111 peptides, 20 chains. Longest chain 8 peptides. Score 0.398 Round 2: 110 peptides, 14 chains. Longest chain 13 peptides. Score 0.554 Round 3: 131 peptides, 15 chains. Longest chain 26 peptides. Score 0.639 Round 4: 124 peptides, 16 chains. Longest chain 21 peptides. Score 0.581 Round 5: 123 peptides, 12 chains. Longest chain 35 peptides. Score 0.666 Taking the results from Round 5 Chains 13, Residues 111, Estimated correctness of the model 57.6 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2847 restraints for refining 1390 atoms. 2351 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3117 (Rfree = 0.000) for 1390 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 22: After refmac, R = 0.2930 (Rfree = 0.000) for 1380 atoms. Found 9 (12 requested) and removed 12 (6 requested) atoms. Cycle 23: After refmac, R = 0.2819 (Rfree = 0.000) for 1372 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2932 (Rfree = 0.000) for 1366 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2814 (Rfree = 0.000) for 1363 atoms. Found 9 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 2.93 Search for helices and strands: 0 residues in 0 chains, 1418 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 1442 seeds are put forward Round 1: 111 peptides, 17 chains. Longest chain 12 peptides. Score 0.481 Round 2: 117 peptides, 15 chains. Longest chain 18 peptides. Score 0.568 Round 3: 122 peptides, 14 chains. Longest chain 22 peptides. Score 0.618 Round 4: 123 peptides, 15 chains. Longest chain 18 peptides. Score 0.600 Round 5: 125 peptides, 14 chains. Longest chain 17 peptides. Score 0.632 Taking the results from Round 5 Chains 14, Residues 111, Estimated correctness of the model 49.4 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2975 restraints for refining 1403 atoms. 2493 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3337 (Rfree = 0.000) for 1403 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 27: After refmac, R = 0.3166 (Rfree = 0.000) for 1395 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2994 (Rfree = 0.000) for 1387 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.3016 (Rfree = 0.000) for 1373 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2911 (Rfree = 0.000) for 1372 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 2.88 Search for helices and strands: 0 residues in 0 chains, 1425 seeds are put forward NCS extension: 0 residues added, 1425 seeds are put forward Round 1: 112 peptides, 18 chains. Longest chain 12 peptides. Score 0.460 Round 2: 115 peptides, 13 chains. Longest chain 20 peptides. Score 0.605 Round 3: 117 peptides, 13 chains. Longest chain 16 peptides. Score 0.616 Round 4: 115 peptides, 12 chains. Longest chain 17 peptides. Score 0.629 Round 5: 103 peptides, 14 chains. Longest chain 19 peptides. Score 0.514 Taking the results from Round 4 Chains 13, Residues 103, Estimated correctness of the model 48.6 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2969 restraints for refining 1393 atoms. 2522 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3051 (Rfree = 0.000) for 1393 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 32: After refmac, R = 0.2916 (Rfree = 0.000) for 1377 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 33: After refmac, R = 0.2888 (Rfree = 0.000) for 1372 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.2807 (Rfree = 0.000) for 1372 atoms. Found 8 (12 requested) and removed 12 (6 requested) atoms. Cycle 35: After refmac, R = 0.2582 (Rfree = 0.000) for 1364 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 2.87 Search for helices and strands: 0 residues in 0 chains, 1407 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 1432 seeds are put forward Round 1: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.376 Round 2: 99 peptides, 14 chains. Longest chain 14 peptides. Score 0.489 Round 3: 101 peptides, 14 chains. Longest chain 13 peptides. Score 0.502 Round 4: 105 peptides, 15 chains. Longest chain 16 peptides. Score 0.499 Round 5: 109 peptides, 13 chains. Longest chain 18 peptides. Score 0.574 Taking the results from Round 5 Chains 13, Residues 96, Estimated correctness of the model 33.9 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2959 restraints for refining 1403 atoms. 2531 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2867 (Rfree = 0.000) for 1403 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 37: After refmac, R = 0.2804 (Rfree = 0.000) for 1396 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2732 (Rfree = 0.000) for 1396 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.2785 (Rfree = 0.000) for 1394 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.2448 (Rfree = 0.000) for 1391 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.01 Search for helices and strands: 0 residues in 0 chains, 1436 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1449 seeds are put forward Round 1: 87 peptides, 13 chains. Longest chain 19 peptides. Score 0.441 Round 2: 102 peptides, 14 chains. Longest chain 21 peptides. Score 0.508 Round 3: 106 peptides, 15 chains. Longest chain 17 peptides. Score 0.505 Round 4: 114 peptides, 14 chains. Longest chain 19 peptides. Score 0.576 Round 5: 104 peptides, 14 chains. Longest chain 14 peptides. Score 0.520 Taking the results from Round 4 Chains 14, Residues 100, Estimated correctness of the model 34.4 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2726 restraints for refining 1379 atoms. 2261 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2895 (Rfree = 0.000) for 1379 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 42: After refmac, R = 0.2931 (Rfree = 0.000) for 1371 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.2761 (Rfree = 0.000) for 1369 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 44: After refmac, R = 0.2822 (Rfree = 0.000) for 1368 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2788 (Rfree = 0.000) for 1365 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 2.86 Search for helices and strands: 0 residues in 0 chains, 1425 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1442 seeds are put forward Round 1: 100 peptides, 17 chains. Longest chain 12 peptides. Score 0.410 Round 2: 111 peptides, 15 chains. Longest chain 16 peptides. Score 0.534 Round 3: 110 peptides, 16 chains. Longest chain 15 peptides. Score 0.502 Round 4: 114 peptides, 16 chains. Longest chain 15 peptides. Score 0.526 Round 5: 114 peptides, 16 chains. Longest chain 15 peptides. Score 0.526 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 96, Estimated correctness of the model 22.1 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2obp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4340 reflections ( 99.47 % complete ) and 2963 restraints for refining 1371 atoms. 2594 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2968 (Rfree = 0.000) for 1371 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2923 (Rfree = 0.000) for 1363 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2962 (Rfree = 0.000) for 1355 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2764 (Rfree = 0.000) for 1348 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:05:56 GMT 2018 Job finished. TimeTaking 42.96 Used memory is bytes: 10251152