Mon 24 Dec 07:31:26 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2obn-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2obn-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2obn-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.8-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:31:30 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/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.8-parrot-noncs/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 836 and 0 Target number of residues in the AU: 836 Target solvent content: 0.6652 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-3.8-parrot-noncs.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: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 11168 target number of atoms Had to go as low as 0.65 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: 73.214 3.800 Wilson plot Bfac: 88.54 13122 reflections ( 99.61 % complete ) and 0 restraints for refining 12405 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2914 (Rfree = 0.000) for 12405 atoms. Found 65 (68 requested) and removed 85 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 12618 seeds are put forward NCS extension: 0 residues added, 12618 seeds are put forward Round 1: 402 peptides, 83 chains. Longest chain 12 peptides. Score 0.270 Round 2: 543 peptides, 100 chains. Longest chain 12 peptides. Score 0.360 Round 3: 599 peptides, 106 chains. Longest chain 15 peptides. Score 0.396 Round 4: 627 peptides, 104 chains. Longest chain 16 peptides. Score 0.439 Round 5: 624 peptides, 99 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 5 Chains 102, Residues 525, Estimated correctness of the model 0.0 % 12 chains (81 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23667 restraints for refining 10095 atoms. 21439 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2302 (Rfree = 0.000) for 10095 atoms. Found 44 (55 requested) and removed 87 (27 requested) atoms. Cycle 2: After refmac, R = 0.2110 (Rfree = 0.000) for 9923 atoms. Found 47 (55 requested) and removed 61 (27 requested) atoms. Cycle 3: After refmac, R = 0.2012 (Rfree = 0.000) for 9839 atoms. Found 30 (54 requested) and removed 46 (27 requested) atoms. Cycle 4: After refmac, R = 0.2024 (Rfree = 0.000) for 9767 atoms. Found 48 (54 requested) and removed 64 (27 requested) atoms. Cycle 5: After refmac, R = 0.1871 (Rfree = 0.000) for 9711 atoms. Found 27 (53 requested) and removed 48 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 10080 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 10102 seeds are put forward Round 1: 538 peptides, 110 chains. Longest chain 13 peptides. Score 0.300 Round 2: 599 peptides, 107 chains. Longest chain 13 peptides. Score 0.391 Round 3: 601 peptides, 99 chains. Longest chain 15 peptides. Score 0.434 Round 4: 631 peptides, 98 chains. Longest chain 14 peptides. Score 0.472 Round 5: 619 peptides, 97 chains. Longest chain 13 peptides. Score 0.463 Taking the results from Round 4 Chains 100, Residues 533, Estimated correctness of the model 0.0 % 13 chains (86 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 22459 restraints for refining 9845 atoms. 20204 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1979 (Rfree = 0.000) for 9845 atoms. Found 36 (54 requested) and removed 88 (27 requested) atoms. Cycle 7: After refmac, R = 0.1883 (Rfree = 0.000) for 9715 atoms. Found 36 (53 requested) and removed 47 (26 requested) atoms. Cycle 8: After refmac, R = 0.1770 (Rfree = 0.000) for 9666 atoms. Found 23 (53 requested) and removed 43 (26 requested) atoms. Cycle 9: After refmac, R = 0.1664 (Rfree = 0.000) for 9626 atoms. Found 26 (53 requested) and removed 41 (26 requested) atoms. Cycle 10: After refmac, R = 0.1642 (Rfree = 0.000) for 9594 atoms. Found 28 (52 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 9882 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 9899 seeds are put forward Round 1: 520 peptides, 103 chains. Longest chain 10 peptides. Score 0.315 Round 2: 617 peptides, 100 chains. Longest chain 15 peptides. Score 0.447 Round 3: 632 peptides, 101 chains. Longest chain 15 peptides. Score 0.459 Round 4: 628 peptides, 97 chains. Longest chain 19 peptides. Score 0.473 Round 5: 635 peptides, 93 chains. Longest chain 24 peptides. Score 0.499 Taking the results from Round 5 Chains 95, Residues 542, Estimated correctness of the model 0.0 % 14 chains (102 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 22837 restraints for refining 10101 atoms. 20461 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1964 (Rfree = 0.000) for 10101 atoms. Found 37 (55 requested) and removed 73 (27 requested) atoms. Cycle 12: After refmac, R = 0.1821 (Rfree = 0.000) for 9973 atoms. Found 35 (55 requested) and removed 48 (27 requested) atoms. Cycle 13: After refmac, R = 0.1706 (Rfree = 0.000) for 9902 atoms. Found 35 (54 requested) and removed 37 (27 requested) atoms. Cycle 14: After refmac, R = 0.1643 (Rfree = 0.000) for 9875 atoms. Found 28 (54 requested) and removed 37 (27 requested) atoms. Cycle 15: After refmac, R = 0.1290 (Rfree = 0.000) for 9845 atoms. Found 12 (54 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 10149 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 10166 seeds are put forward Round 1: 526 peptides, 109 chains. Longest chain 11 peptides. Score 0.290 Round 2: 590 peptides, 105 chains. Longest chain 13 peptides. Score 0.391 Round 3: 605 peptides, 106 chains. Longest chain 14 peptides. Score 0.403 Round 4: 584 peptides, 97 chains. Longest chain 13 peptides. Score 0.424 Round 5: 602 peptides, 102 chains. Longest chain 16 peptides. Score 0.420 Taking the results from Round 4 Chains 99, Residues 487, Estimated correctness of the model 0.0 % 11 chains (58 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23506 restraints for refining 10100 atoms. 21519 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1946 (Rfree = 0.000) for 10100 atoms. Found 51 (55 requested) and removed 88 (27 requested) atoms. Cycle 17: After refmac, R = 0.1651 (Rfree = 0.000) for 10008 atoms. Found 42 (55 requested) and removed 43 (27 requested) atoms. Cycle 18: After refmac, R = 0.1311 (Rfree = 0.000) for 9975 atoms. Found 11 (55 requested) and removed 38 (27 requested) atoms. Cycle 19: After refmac, R = 0.1207 (Rfree = 0.000) for 9930 atoms. Found 3 (54 requested) and removed 32 (27 requested) atoms. Cycle 20: After refmac, R = 0.1318 (Rfree = 0.000) for 9893 atoms. Found 8 (54 requested) and removed 41 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 10136 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 10151 seeds are put forward Round 1: 483 peptides, 103 chains. Longest chain 9 peptides. Score 0.266 Round 2: 562 peptides, 103 chains. Longest chain 14 peptides. Score 0.367 Round 3: 570 peptides, 96 chains. Longest chain 16 peptides. Score 0.413 Round 4: 571 peptides, 96 chains. Longest chain 13 peptides. Score 0.414 Round 5: 558 peptides, 90 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 5 Chains 90, Residues 468, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23936 restraints for refining 10101 atoms. 22146 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1665 (Rfree = 0.000) for 10101 atoms. Found 25 (55 requested) and removed 51 (27 requested) atoms. Cycle 22: After refmac, R = 0.1705 (Rfree = 0.000) for 10014 atoms. Found 51 (55 requested) and removed 45 (27 requested) atoms. Cycle 23: After refmac, R = 0.1651 (Rfree = 0.000) for 9979 atoms. Found 51 (55 requested) and removed 53 (27 requested) atoms. Cycle 24: After refmac, R = 0.1191 (Rfree = 0.000) for 9950 atoms. Found 12 (54 requested) and removed 36 (27 requested) atoms. Cycle 25: After refmac, R = 0.1066 (Rfree = 0.000) for 9914 atoms. Found 7 (54 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 10233 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 10248 seeds are put forward Round 1: 476 peptides, 98 chains. Longest chain 12 peptides. Score 0.285 Round 2: 580 peptides, 106 chains. Longest chain 15 peptides. Score 0.374 Round 3: 563 peptides, 99 chains. Longest chain 17 peptides. Score 0.389 Round 4: 553 peptides, 98 chains. Longest chain 14 peptides. Score 0.382 Round 5: 578 peptides, 100 chains. Longest chain 16 peptides. Score 0.402 Taking the results from Round 5 Chains 102, Residues 478, Estimated correctness of the model 0.0 % 7 chains (42 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23614 restraints for refining 10099 atoms. 21691 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1671 (Rfree = 0.000) for 10099 atoms. Found 33 (55 requested) and removed 52 (27 requested) atoms. Cycle 27: After refmac, R = 0.1557 (Rfree = 0.000) for 10029 atoms. Found 42 (55 requested) and removed 45 (27 requested) atoms. Cycle 28: After refmac, R = 0.1493 (Rfree = 0.000) for 10007 atoms. Found 33 (55 requested) and removed 37 (27 requested) atoms. Cycle 29: After refmac, R = 0.1486 (Rfree = 0.000) for 9974 atoms. Found 40 (55 requested) and removed 38 (27 requested) atoms. Cycle 30: After refmac, R = 0.1430 (Rfree = 0.000) for 9951 atoms. Found 45 (54 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 10232 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 10246 seeds are put forward Round 1: 435 peptides, 94 chains. Longest chain 9 peptides. Score 0.252 Round 2: 495 peptides, 95 chains. Longest chain 12 peptides. Score 0.326 Round 3: 506 peptides, 93 chains. Longest chain 13 peptides. Score 0.351 Round 4: 504 peptides, 89 chains. Longest chain 13 peptides. Score 0.370 Round 5: 494 peptides, 87 chains. Longest chain 13 peptides. Score 0.368 Taking the results from Round 4 Chains 89, Residues 415, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 24273 restraints for refining 10101 atoms. 22662 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1672 (Rfree = 0.000) for 10101 atoms. Found 44 (55 requested) and removed 54 (27 requested) atoms. Cycle 32: After refmac, R = 0.1604 (Rfree = 0.000) for 10059 atoms. Found 55 (55 requested) and removed 43 (27 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1562 (Rfree = 0.000) for 10044 atoms. Found 55 (55 requested) and removed 51 (27 requested) atoms. Cycle 34: After refmac, R = 0.1488 (Rfree = 0.000) for 10034 atoms. Found 55 (55 requested) and removed 48 (27 requested) atoms. Cycle 35: After refmac, R = 0.1538 (Rfree = 0.000) for 10031 atoms. Found 55 (55 requested) and removed 46 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 10302 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 10318 seeds are put forward Round 1: 372 peptides, 82 chains. Longest chain 12 peptides. Score 0.233 Round 2: 417 peptides, 79 chains. Longest chain 11 peptides. Score 0.313 Round 3: 466 peptides, 88 chains. Longest chain 12 peptides. Score 0.327 Round 4: 456 peptides, 82 chains. Longest chain 13 peptides. Score 0.347 Round 5: 468 peptides, 84 chains. Longest chain 14 peptides. Score 0.352 Taking the results from Round 5 Chains 86, Residues 384, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 24340 restraints for refining 10101 atoms. 22835 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1545 (Rfree = 0.000) for 10101 atoms. Found 41 (55 requested) and removed 55 (27 requested) atoms. Cycle 37: After refmac, R = 0.1504 (Rfree = 0.000) for 10052 atoms. Found 52 (55 requested) and removed 48 (27 requested) atoms. Cycle 38: After refmac, R = 0.1471 (Rfree = 0.000) for 10043 atoms. Found 46 (55 requested) and removed 44 (27 requested) atoms. Cycle 39: After refmac, R = 0.1029 (Rfree = 0.000) for 10035 atoms. Found 11 (55 requested) and removed 32 (27 requested) atoms. Cycle 40: After refmac, R = 0.0958 (Rfree = 0.000) for 10006 atoms. Found 12 (55 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 10268 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 10283 seeds are put forward Round 1: 337 peptides, 74 chains. Longest chain 11 peptides. Score 0.230 Round 2: 414 peptides, 84 chains. Longest chain 11 peptides. Score 0.280 Round 3: 415 peptides, 82 chains. Longest chain 12 peptides. Score 0.293 Round 4: 401 peptides, 78 chains. Longest chain 12 peptides. Score 0.297 Round 5: 394 peptides, 74 chains. Longest chain 12 peptides. Score 0.311 Taking the results from Round 5 Chains 74, Residues 320, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 24721 restraints for refining 10101 atoms. 23478 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1633 (Rfree = 0.000) for 10101 atoms. Found 55 (55 requested) and removed 45 (27 requested) atoms. Cycle 42: After refmac, R = 0.1554 (Rfree = 0.000) for 10079 atoms. Found 45 (55 requested) and removed 34 (27 requested) atoms. Cycle 43: After refmac, R = 0.1489 (Rfree = 0.000) for 10071 atoms. Found 48 (55 requested) and removed 38 (27 requested) atoms. Cycle 44: After refmac, R = 0.1378 (Rfree = 0.000) for 10069 atoms. Found 38 (55 requested) and removed 38 (27 requested) atoms. Cycle 45: After refmac, R = 0.1042 (Rfree = 0.000) for 10058 atoms. Found 9 (55 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 10269 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 10283 seeds are put forward Round 1: 330 peptides, 75 chains. Longest chain 8 peptides. Score 0.214 Round 2: 391 peptides, 81 chains. Longest chain 9 peptides. Score 0.266 Round 3: 393 peptides, 75 chains. Longest chain 11 peptides. Score 0.304 Round 4: 385 peptides, 70 chains. Longest chain 11 peptides. Score 0.322 Round 5: 384 peptides, 73 chains. Longest chain 11 peptides. Score 0.303 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 315, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 70 chains (315 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13122 reflections ( 99.61 % complete ) and 24657 restraints for refining 10101 atoms. 23428 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1421 (Rfree = 0.000) for 10101 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1484 (Rfree = 0.000) for 10061 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1478 (Rfree = 0.000) for 10024 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1390 (Rfree = 0.000) for 9988 atoms. TimeTaking 99.17