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 2ou6-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.4-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/2ou6-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.4-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 22:22:56 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/2ou6-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.4-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 170 and 0 Target number of residues in the AU: 170 Target solvent content: 0.6213 Checking the provided sequence file Detected sequence length: 190 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 190 Adjusted target solvent content: 0.58 Input MTZ file: 2ou6-3.4-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: 179 Cell parameters: 57.933 57.933 250.773 90.000 90.000 120.000 Input sequence file: 2ou6-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.85 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: 50.171 3.400 Wilson plot Bfac: 61.31 3905 reflections ( 99.80 % complete ) and 0 restraints for refining 1682 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3604 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3342 (Rfree = 0.000) for 1682 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 2.92 Search for helices and strands: 0 residues in 0 chains, 1727 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.307 Round 2: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.379 Round 3: 112 peptides, 16 chains. Longest chain 14 peptides. Score 0.505 Round 4: 120 peptides, 13 chains. Longest chain 21 peptides. Score 0.620 Round 5: 127 peptides, 16 chains. Longest chain 18 peptides. Score 0.587 Taking the results from Round 4 Chains 15, Residues 107, Estimated correctness of the model 35.1 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 3905 reflections ( 99.80 % complete ) and 2656 restraints for refining 1381 atoms. 2119 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3221 (Rfree = 0.000) for 1381 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 2: After refmac, R = 0.2983 (Rfree = 0.000) for 1344 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.2899 (Rfree = 0.000) for 1329 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 4: After refmac, R = 0.2856 (Rfree = 0.000) for 1327 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2840 (Rfree = 0.000) for 1322 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 2.94 Search for helices and strands: 0 residues in 0 chains, 1383 seeds are put forward Round 1: 108 peptides, 18 chains. Longest chain 12 peptides. Score 0.428 Round 2: 120 peptides, 16 chains. Longest chain 15 peptides. Score 0.550 Round 3: 117 peptides, 13 chains. Longest chain 18 peptides. Score 0.605 Round 4: 118 peptides, 13 chains. Longest chain 16 peptides. Score 0.610 Round 5: 123 peptides, 13 chains. Longest chain 16 peptides. Score 0.634 Taking the results from Round 5 Chains 13, Residues 110, Estimated correctness of the model 39.4 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3905 reflections ( 99.80 % complete ) and 2855 restraints for refining 1382 atoms. 2373 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2953 (Rfree = 0.000) for 1382 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 7: After refmac, R = 0.2830 (Rfree = 0.000) for 1375 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.2720 (Rfree = 0.000) for 1369 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 9: After refmac, R = 0.2559 (Rfree = 0.000) for 1369 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2539 (Rfree = 0.000) for 1361 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 1434 seeds are put forward Round 1: 112 peptides, 17 chains. Longest chain 15 peptides. Score 0.479 Round 2: 108 peptides, 15 chains. Longest chain 16 peptides. Score 0.508 Round 3: 116 peptides, 18 chains. Longest chain 12 peptides. Score 0.477 Round 4: 111 peptides, 12 chains. Longest chain 20 peptides. Score 0.599 Round 5: 125 peptides, 15 chains. Longest chain 20 peptides. Score 0.599 Taking the results from Round 5 Chains 19, Residues 110, Estimated correctness of the model 28.3 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3905 reflections ( 99.80 % complete ) and 2721 restraints for refining 1382 atoms. 2189 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3072 (Rfree = 0.000) for 1382 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 12: After refmac, R = 0.2869 (Rfree = 0.000) for 1377 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2851 (Rfree = 0.000) for 1366 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2772 (Rfree = 0.000) for 1366 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.2674 (Rfree = 0.000) for 1362 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 1421 seeds are put forward Round 1: 113 peptides, 17 chains. Longest chain 13 peptides. Score 0.485 Round 2: 119 peptides, 16 chains. Longest chain 11 peptides. Score 0.545 Round 3: 129 peptides, 18 chains. Longest chain 16 peptides. Score 0.551 Round 4: 125 peptides, 15 chains. Longest chain 17 peptides. Score 0.599 Round 5: 107 peptides, 15 chains. Longest chain 11 peptides. Score 0.502 Taking the results from Round 4 Chains 16, Residues 110, Estimated correctness of the model 28.3 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3905 reflections ( 99.80 % complete ) and 2934 restraints for refining 1382 atoms. 2455 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3009 (Rfree = 0.000) for 1382 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 17: After refmac, R = 0.2877 (Rfree = 0.000) for 1373 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.2740 (Rfree = 0.000) for 1371 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2634 (Rfree = 0.000) for 1367 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.2637 (Rfree = 0.000) for 1367 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 1431 seeds are put forward Round 1: 103 peptides, 15 chains. Longest chain 14 peptides. Score 0.478 Round 2: 116 peptides, 16 chains. Longest chain 17 peptides. Score 0.528 Round 3: 122 peptides, 15 chains. Longest chain 19 peptides. Score 0.584 Round 4: 122 peptides, 16 chains. Longest chain 16 peptides. Score 0.561 Round 5: 124 peptides, 16 chains. Longest chain 15 peptides. Score 0.571 Taking the results from Round 3 Chains 16, Residues 107, Estimated correctness of the model 23.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3905 reflections ( 99.80 % complete ) and 2751 restraints for refining 1382 atoms. 2246 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2912 (Rfree = 0.000) for 1382 atoms. Found 7 (10 requested) and removed 11 (5 requested) atoms. Cycle 22: After refmac, R = 0.2787 (Rfree = 0.000) for 1370 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2722 (Rfree = 0.000) for 1367 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.2639 (Rfree = 0.000) for 1364 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2639 (Rfree = 0.000) for 1363 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.80 Search for helices and strands: 0 residues in 0 chains, 1428 seeds are put forward Round 1: 115 peptides, 18 chains. Longest chain 15 peptides. Score 0.471 Round 2: 113 peptides, 16 chains. Longest chain 16 peptides. Score 0.511 Round 3: 117 peptides, 15 chains. Longest chain 18 peptides. Score 0.558 Round 4: 118 peptides, 16 chains. Longest chain 19 peptides. Score 0.539 Round 5: 109 peptides, 15 chains. Longest chain 16 peptides. Score 0.514 Taking the results from Round 3 Chains 15, Residues 102, Estimated correctness of the model 14.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3905 reflections ( 99.80 % complete ) and 3064 restraints for refining 1382 atoms. 2671 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2934 (Rfree = 0.000) for 1382 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 27: After refmac, R = 0.2768 (Rfree = 0.000) for 1381 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2793 (Rfree = 0.000) for 1383 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2529 (Rfree = 0.000) for 1382 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2469 (Rfree = 0.000) for 1384 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 2.90 Search for helices and strands: 0 residues in 0 chains, 1462 seeds are put forward Round 1: 98 peptides, 17 chains. Longest chain 16 peptides. Score 0.391 Round 2: 103 peptides, 14 chains. Longest chain 18 peptides. Score 0.505 Round 3: 112 peptides, 15 chains. Longest chain 19 peptides. Score 0.531 Round 4: 118 peptides, 14 chains. Longest chain 20 peptides. Score 0.587 Round 5: 109 peptides, 15 chains. Longest chain 13 peptides. Score 0.514 Taking the results from Round 4 Chains 15, Residues 104, Estimated correctness of the model 24.4 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3905 reflections ( 99.80 % complete ) and 2899 restraints for refining 1382 atoms. 2422 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2890 (Rfree = 0.000) for 1382 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 32: After refmac, R = 0.2778 (Rfree = 0.000) for 1376 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.2696 (Rfree = 0.000) for 1374 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.2631 (Rfree = 0.000) for 1375 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2597 (Rfree = 0.000) for 1377 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 1439 seeds are put forward Round 1: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.382 Round 2: 108 peptides, 16 chains. Longest chain 17 peptides. Score 0.482 Round 3: 113 peptides, 15 chains. Longest chain 13 peptides. Score 0.536 Round 4: 116 peptides, 16 chains. Longest chain 15 peptides. Score 0.528 Round 5: 121 peptides, 18 chains. Longest chain 17 peptides. Score 0.506 Taking the results from Round 3 Chains 15, Residues 98, Estimated correctness of the model 6.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3905 reflections ( 99.80 % complete ) and 3030 restraints for refining 1382 atoms. 2653 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2720 (Rfree = 0.000) for 1382 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.2559 (Rfree = 0.000) for 1380 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.2477 (Rfree = 0.000) for 1378 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.2469 (Rfree = 0.000) for 1378 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2429 (Rfree = 0.000) for 1377 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 1443 seeds are put forward Round 1: 101 peptides, 18 chains. Longest chain 16 peptides. Score 0.382 Round 2: 115 peptides, 18 chains. Longest chain 21 peptides. Score 0.471 Round 3: 110 peptides, 17 chains. Longest chain 14 peptides. Score 0.467 Round 4: 115 peptides, 16 chains. Longest chain 17 peptides. Score 0.523 Round 5: 111 peptides, 19 chains. Longest chain 10 peptides. Score 0.419 Taking the results from Round 4 Chains 17, Residues 99, Estimated correctness of the model 1.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3905 reflections ( 99.80 % complete ) and 2927 restraints for refining 1382 atoms. 2513 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2706 (Rfree = 0.000) for 1382 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2649 (Rfree = 0.000) for 1384 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.2561 (Rfree = 0.000) for 1386 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2505 (Rfree = 0.000) for 1386 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2468 (Rfree = 0.000) for 1387 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 1450 seeds are put forward Round 1: 95 peptides, 17 chains. Longest chain 12 peptides. Score 0.370 Round 2: 108 peptides, 18 chains. Longest chain 10 peptides. Score 0.428 Round 3: 101 peptides, 16 chains. Longest chain 13 peptides. Score 0.439 Round 4: 109 peptides, 17 chains. Longest chain 9 peptides. Score 0.461 Round 5: 101 peptides, 15 chains. Longest chain 12 peptides. Score 0.466 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 86, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2ou6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3905 reflections ( 99.80 % complete ) and 3038 restraints for refining 1382 atoms. 2665 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2556 (Rfree = 0.000) for 1382 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2623 (Rfree = 0.000) for 1376 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2432 (Rfree = 0.000) for 1369 atoms. Found 0 (10 requested) and removed 4 (5 requested) atoms. Cycle 49: After refmac, R = 0.2528 (Rfree = 0.000) for 1362 atoms. Found 0 (10 requested) and removed 1 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:59 GMT 2018 Job finished. TimeTaking 30.22 Used memory is bytes: 15561792