Mon 24 Dec 00:53:05 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 2obn-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.8-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/2obn-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.8-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 ============================================================ Mon 24 Dec 00:53:10 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/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.8-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 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-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: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.8-parrot-mrncs.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 12397 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3108 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3015 (Rfree = 0.000) for 12397 atoms. Found 68 (68 requested) and removed 70 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 12643 seeds are put forward NCS extension: 0 residues added, 12643 seeds are put forward Round 1: 385 peptides, 77 chains. Longest chain 13 peptides. Score 0.281 Round 2: 552 peptides, 96 chains. Longest chain 17 peptides. Score 0.391 Round 3: 626 peptides, 103 chains. Longest chain 16 peptides. Score 0.442 Round 4: 678 peptides, 106 chains. Longest chain 18 peptides. Score 0.485 Round 5: 726 peptides, 109 chains. Longest chain 17 peptides. Score 0.521 Taking the results from Round 5 Chains 112, Residues 617, Estimated correctness of the model 0.0 % 10 chains (71 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23281 restraints for refining 10100 atoms. 20740 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2294 (Rfree = 0.000) for 10100 atoms. Found 37 (55 requested) and removed 71 (27 requested) atoms. Cycle 2: After refmac, R = 0.2104 (Rfree = 0.000) for 9881 atoms. Found 36 (55 requested) and removed 46 (27 requested) atoms. Cycle 3: After refmac, R = 0.2019 (Rfree = 0.000) for 9797 atoms. Found 27 (54 requested) and removed 50 (27 requested) atoms. Cycle 4: After refmac, R = 0.1923 (Rfree = 0.000) for 9727 atoms. Found 28 (53 requested) and removed 44 (26 requested) atoms. Cycle 5: After refmac, R = 0.1646 (Rfree = 0.000) for 9677 atoms. Found 14 (53 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 4.03 Search for helices and strands: 0 residues in 0 chains, 10003 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 10020 seeds are put forward Round 1: 571 peptides, 110 chains. Longest chain 13 peptides. Score 0.342 Round 2: 651 peptides, 95 chains. Longest chain 22 peptides. Score 0.507 Round 3: 693 peptides, 96 chains. Longest chain 20 peptides. Score 0.545 Round 4: 674 peptides, 104 chains. Longest chain 19 peptides. Score 0.490 Round 5: 704 peptides, 102 chains. Longest chain 21 peptides. Score 0.529 Taking the results from Round 3 Chains 101, Residues 597, Estimated correctness of the model 0.0 % 14 chains (89 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 22094 restraints for refining 9812 atoms. 19555 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2133 (Rfree = 0.000) for 9812 atoms. Found 41 (53 requested) and removed 80 (26 requested) atoms. Cycle 7: After refmac, R = 0.1963 (Rfree = 0.000) for 9698 atoms. Found 42 (53 requested) and removed 33 (26 requested) atoms. Cycle 8: After refmac, R = 0.1854 (Rfree = 0.000) for 9676 atoms. Found 31 (53 requested) and removed 48 (26 requested) atoms. Cycle 9: After refmac, R = 0.1793 (Rfree = 0.000) for 9610 atoms. Found 34 (53 requested) and removed 41 (26 requested) atoms. Cycle 10: After refmac, R = 0.1824 (Rfree = 0.000) for 9583 atoms. Found 38 (52 requested) and removed 41 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 9911 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 9932 seeds are put forward Round 1: 587 peptides, 112 chains. Longest chain 17 peptides. Score 0.351 Round 2: 684 peptides, 106 chains. Longest chain 18 peptides. Score 0.491 Round 3: 700 peptides, 107 chains. Longest chain 20 peptides. Score 0.503 Round 4: 705 peptides, 107 chains. Longest chain 20 peptides. Score 0.508 Round 5: 701 peptides, 109 chains. Longest chain 18 peptides. Score 0.495 Taking the results from Round 4 Chains 111, Residues 598, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 22837 restraints for refining 9873 atoms. 20460 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2106 (Rfree = 0.000) for 9873 atoms. Found 47 (54 requested) and removed 83 (27 requested) atoms. Cycle 12: After refmac, R = 0.1851 (Rfree = 0.000) for 9743 atoms. Found 29 (54 requested) and removed 55 (27 requested) atoms. Cycle 13: After refmac, R = 0.1740 (Rfree = 0.000) for 9671 atoms. Found 31 (53 requested) and removed 37 (26 requested) atoms. Cycle 14: After refmac, R = 0.1720 (Rfree = 0.000) for 9647 atoms. Found 28 (53 requested) and removed 41 (26 requested) atoms. Cycle 15: After refmac, R = 0.1382 (Rfree = 0.000) for 9613 atoms. Found 7 (52 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 9904 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 9933 seeds are put forward Round 1: 577 peptides, 113 chains. Longest chain 16 peptides. Score 0.334 Round 2: 610 peptides, 100 chains. Longest chain 21 peptides. Score 0.439 Round 3: 618 peptides, 103 chains. Longest chain 18 peptides. Score 0.433 Round 4: 649 peptides, 99 chains. Longest chain 22 peptides. Score 0.486 Round 5: 651 peptides, 100 chains. Longest chain 22 peptides. Score 0.484 Taking the results from Round 4 Chains 104, Residues 550, Estimated correctness of the model 0.0 % 15 chains (98 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 22427 restraints for refining 9971 atoms. 20062 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1853 (Rfree = 0.000) for 9971 atoms. Found 40 (54 requested) and removed 70 (27 requested) atoms. Cycle 17: After refmac, R = 0.1665 (Rfree = 0.000) for 9878 atoms. Found 42 (54 requested) and removed 55 (27 requested) atoms. Cycle 18: After refmac, R = 0.1612 (Rfree = 0.000) for 9839 atoms. Found 32 (54 requested) and removed 43 (27 requested) atoms. Cycle 19: After refmac, R = 0.1630 (Rfree = 0.000) for 9801 atoms. Found 37 (54 requested) and removed 43 (27 requested) atoms. Cycle 20: After refmac, R = 0.1583 (Rfree = 0.000) for 9776 atoms. Found 37 (53 requested) and removed 40 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 10093 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 10104 seeds are put forward Round 1: 525 peptides, 108 chains. Longest chain 17 peptides. Score 0.294 Round 2: 590 peptides, 102 chains. Longest chain 16 peptides. Score 0.406 Round 3: 618 peptides, 106 chains. Longest chain 12 peptides. Score 0.418 Round 4: 607 peptides, 99 chains. Longest chain 17 peptides. Score 0.440 Round 5: 623 peptides, 99 chains. Longest chain 17 peptides. Score 0.458 Taking the results from Round 5 Chains 103, Residues 524, Estimated correctness of the model 0.0 % 8 chains (50 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23446 restraints for refining 10100 atoms. 21307 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1936 (Rfree = 0.000) for 10100 atoms. Found 52 (55 requested) and removed 64 (27 requested) atoms. Cycle 22: After refmac, R = 0.1777 (Rfree = 0.000) for 10036 atoms. Found 55 (55 requested) and removed 56 (27 requested) atoms. Cycle 23: After refmac, R = 0.1735 (Rfree = 0.000) for 10004 atoms. Found 47 (55 requested) and removed 50 (27 requested) atoms. Cycle 24: After refmac, R = 0.1354 (Rfree = 0.000) for 9971 atoms. Found 3 (54 requested) and removed 37 (27 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1272 (Rfree = 0.000) for 9928 atoms. Found 7 (54 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 10225 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 10241 seeds are put forward Round 1: 430 peptides, 87 chains. Longest chain 10 peptides. Score 0.285 Round 2: 524 peptides, 95 chains. Longest chain 12 peptides. Score 0.363 Round 3: 547 peptides, 96 chains. Longest chain 13 peptides. Score 0.385 Round 4: 554 peptides, 90 chains. Longest chain 15 peptides. Score 0.425 Round 5: 571 peptides, 89 chains. Longest chain 15 peptides. Score 0.449 Taking the results from Round 5 Chains 89, Residues 482, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23975 restraints for refining 10101 atoms. 22102 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1978 (Rfree = 0.000) for 10101 atoms. Found 55 (55 requested) and removed 56 (27 requested) atoms. Cycle 27: After refmac, R = 0.1777 (Rfree = 0.000) for 10055 atoms. Found 51 (55 requested) and removed 38 (27 requested) atoms. Cycle 28: After refmac, R = 0.1788 (Rfree = 0.000) for 10029 atoms. Found 55 (55 requested) and removed 43 (27 requested) atoms. Cycle 29: After refmac, R = 0.1286 (Rfree = 0.000) for 10015 atoms. Found 14 (55 requested) and removed 33 (27 requested) atoms. Cycle 30: After refmac, R = 0.1184 (Rfree = 0.000) for 9979 atoms. Found 8 (54 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 10255 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10269 seeds are put forward Round 1: 440 peptides, 93 chains. Longest chain 13 peptides. Score 0.264 Round 2: 510 peptides, 95 chains. Longest chain 13 peptides. Score 0.345 Round 3: 484 peptides, 87 chains. Longest chain 14 peptides. Score 0.356 Round 4: 482 peptides, 87 chains. Longest chain 13 peptides. Score 0.353 Round 5: 482 peptides, 84 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 5 Chains 84, Residues 398, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13122 reflections ( 99.61 % complete ) and 24654 restraints for refining 10101 atoms. 23131 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1717 (Rfree = 0.000) for 10101 atoms. Found 42 (55 requested) and removed 41 (27 requested) atoms. Cycle 32: After refmac, R = 0.1745 (Rfree = 0.000) for 10060 atoms. Found 55 (55 requested) and removed 38 (27 requested) atoms. Cycle 33: After refmac, R = 0.1693 (Rfree = 0.000) for 10050 atoms. Found 52 (55 requested) and removed 34 (27 requested) atoms. Cycle 34: After refmac, R = 0.1659 (Rfree = 0.000) for 10041 atoms. Found 55 (55 requested) and removed 39 (27 requested) atoms. Cycle 35: After refmac, R = 0.1168 (Rfree = 0.000) for 10042 atoms. Found 14 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 10316 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10330 seeds are put forward Round 1: 384 peptides, 84 chains. Longest chain 10 peptides. Score 0.238 Round 2: 434 peptides, 80 chains. Longest chain 14 peptides. Score 0.330 Round 3: 443 peptides, 80 chains. Longest chain 15 peptides. Score 0.342 Round 4: 461 peptides, 85 chains. Longest chain 13 peptides. Score 0.337 Round 5: 464 peptides, 85 chains. Longest chain 14 peptides. Score 0.341 Taking the results from Round 3 Chains 83, Residues 363, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 24255 restraints for refining 10055 atoms. 22813 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1681 (Rfree = 0.000) for 10055 atoms. Found 55 (55 requested) and removed 49 (27 requested) atoms. Cycle 37: After refmac, R = 0.1686 (Rfree = 0.000) for 10026 atoms. Found 55 (55 requested) and removed 40 (27 requested) atoms. Cycle 38: After refmac, R = 0.1205 (Rfree = 0.000) for 10023 atoms. Found 13 (55 requested) and removed 37 (27 requested) atoms. Cycle 39: After refmac, R = 0.1089 (Rfree = 0.000) for 9981 atoms. Found 9 (54 requested) and removed 29 (27 requested) atoms. Cycle 40: After refmac, R = 0.1083 (Rfree = 0.000) for 9952 atoms. Found 5 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 10220 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 10236 seeds are put forward Round 1: 376 peptides, 82 chains. Longest chain 11 peptides. Score 0.239 Round 2: 414 peptides, 81 chains. Longest chain 12 peptides. Score 0.298 Round 3: 449 peptides, 86 chains. Longest chain 12 peptides. Score 0.316 Round 4: 453 peptides, 83 chains. Longest chain 12 peptides. Score 0.338 Round 5: 445 peptides, 82 chains. Longest chain 12 peptides. Score 0.333 Taking the results from Round 4 Chains 83, Residues 370, Estimated correctness of the model 0.0 % 8 chains (31 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 24315 restraints for refining 10100 atoms. 22829 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1772 (Rfree = 0.000) for 10100 atoms. Found 55 (55 requested) and removed 56 (27 requested) atoms. Cycle 42: After refmac, R = 0.1711 (Rfree = 0.000) for 10051 atoms. Found 55 (55 requested) and removed 39 (27 requested) atoms. Cycle 43: After refmac, R = 0.1784 (Rfree = 0.000) for 10036 atoms. Found 55 (55 requested) and removed 36 (27 requested) atoms. Cycle 44: After refmac, R = 0.1251 (Rfree = 0.000) for 10040 atoms. Found 12 (55 requested) and removed 30 (27 requested) atoms. Cycle 45: After refmac, R = 0.1090 (Rfree = 0.000) for 10009 atoms. Found 18 (55 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 10252 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 10267 seeds are put forward Round 1: 347 peptides, 77 chains. Longest chain 12 peptides. Score 0.227 Round 2: 392 peptides, 76 chains. Longest chain 12 peptides. Score 0.297 Round 3: 418 peptides, 80 chains. Longest chain 12 peptides. Score 0.309 Round 4: 428 peptides, 81 chains. Longest chain 12 peptides. Score 0.317 Round 5: 425 peptides, 77 chains. Longest chain 12 peptides. Score 0.335 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 77, Residues 348, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 77 chains (348 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13122 reflections ( 99.61 % complete ) and 24890 restraints for refining 10101 atoms. 23557 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1721 (Rfree = 0.000) for 10101 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1767 (Rfree = 0.000) for 10054 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1622 (Rfree = 0.000) for 10005 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1590 (Rfree = 0.000) for 9958 atoms. TimeTaking 110.23