null Tue 25 Dec 19:27:56 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 2obn-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obn-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obn-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-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/2obn-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-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 ============================================================ Tue 25 Dec 19:28:11 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/2obn-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-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 807 and 0 Target number of residues in the AU: 807 Target solvent content: 0.6768 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-4.0-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: 4 Cell parameters: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-4.0-parrot-hancs.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 4.000 Wilson plot Bfac: 98.12 11286 reflections ( 99.58 % complete ) and 0 restraints for refining 12382 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3176 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3070 (Rfree = 0.000) for 12382 atoms. Found 58 (58 requested) and removed 84 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.86 4.18 Search for helices and strands: 0 residues in 0 chains, 12585 seeds are put forward NCS extension: 0 residues added, 12585 seeds are put forward Round 1: 378 peptides, 82 chains. Longest chain 8 peptides. Score 0.242 Round 2: 507 peptides, 92 chains. Longest chain 14 peptides. Score 0.357 Round 3: 548 peptides, 91 chains. Longest chain 15 peptides. Score 0.412 Round 4: 587 peptides, 99 chains. Longest chain 13 peptides. Score 0.417 Round 5: 613 peptides, 93 chains. Longest chain 15 peptides. Score 0.476 Taking the results from Round 5 Chains 93, Residues 520, Estimated correctness of the model 0.0 % 12 chains (87 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 23811 restraints for refining 10082 atoms. 21565 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2351 (Rfree = 0.000) for 10082 atoms. Found 47 (47 requested) and removed 100 (23 requested) atoms. Cycle 2: After refmac, R = 0.2070 (Rfree = 0.000) for 9875 atoms. Found 25 (47 requested) and removed 86 (23 requested) atoms. Cycle 3: After refmac, R = 0.2091 (Rfree = 0.000) for 9739 atoms. Found 31 (46 requested) and removed 64 (23 requested) atoms. Cycle 4: After refmac, R = 0.1933 (Rfree = 0.000) for 9658 atoms. Found 25 (46 requested) and removed 48 (23 requested) atoms. Cycle 5: After refmac, R = 0.1927 (Rfree = 0.000) for 9593 atoms. Found 38 (45 requested) and removed 55 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 4.15 Search for helices and strands: 0 residues in 0 chains, 9941 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 9958 seeds are put forward Round 1: 491 peptides, 103 chains. Longest chain 10 peptides. Score 0.277 Round 2: 594 peptides, 101 chains. Longest chain 13 peptides. Score 0.416 Round 3: 623 peptides, 99 chains. Longest chain 12 peptides. Score 0.458 Round 4: 645 peptides, 96 chains. Longest chain 15 peptides. Score 0.496 Round 5: 661 peptides, 100 chains. Longest chain 15 peptides. Score 0.494 Taking the results from Round 4 Chains 99, Residues 549, Estimated correctness of the model 0.0 % 7 chains (50 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22888 restraints for refining 9852 atoms. 20679 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1994 (Rfree = 0.000) for 9852 atoms. Found 39 (46 requested) and removed 83 (23 requested) atoms. Cycle 7: After refmac, R = 0.1962 (Rfree = 0.000) for 9723 atoms. Found 46 (46 requested) and removed 74 (23 requested) atoms. Cycle 8: After refmac, R = 0.1831 (Rfree = 0.000) for 9628 atoms. Found 43 (46 requested) and removed 69 (23 requested) atoms. Cycle 9: After refmac, R = 0.1712 (Rfree = 0.000) for 9570 atoms. Found 31 (45 requested) and removed 38 (22 requested) atoms. Cycle 10: After refmac, R = 0.1718 (Rfree = 0.000) for 9529 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.88 4.20 Search for helices and strands: 0 residues in 0 chains, 9848 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 9867 seeds are put forward Round 1: 523 peptides, 103 chains. Longest chain 11 peptides. Score 0.319 Round 2: 596 peptides, 102 chains. Longest chain 14 peptides. Score 0.413 Round 3: 603 peptides, 96 chains. Longest chain 16 peptides. Score 0.451 Round 4: 611 peptides, 97 chains. Longest chain 14 peptides. Score 0.455 Round 5: 588 peptides, 90 chains. Longest chain 14 peptides. Score 0.463 Taking the results from Round 5 Chains 93, Residues 498, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 23782 restraints for refining 10048 atoms. 21790 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1909 (Rfree = 0.000) for 10048 atoms. Found 39 (47 requested) and removed 82 (23 requested) atoms. Cycle 12: After refmac, R = 0.1833 (Rfree = 0.000) for 9928 atoms. Found 43 (47 requested) and removed 72 (23 requested) atoms. Cycle 13: After refmac, R = 0.1697 (Rfree = 0.000) for 9858 atoms. Found 43 (47 requested) and removed 47 (23 requested) atoms. Cycle 14: After refmac, R = 0.1210 (Rfree = 0.000) for 9823 atoms. Found 13 (46 requested) and removed 27 (23 requested) atoms. Cycle 15: After refmac, R = 0.1169 (Rfree = 0.000) for 9790 atoms. Found 15 (46 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.88 4.20 Search for helices and strands: 0 residues in 0 chains, 10093 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 10109 seeds are put forward Round 1: 481 peptides, 101 chains. Longest chain 10 peptides. Score 0.275 Round 2: 563 peptides, 104 chains. Longest chain 13 peptides. Score 0.363 Round 3: 576 peptides, 97 chains. Longest chain 16 peptides. Score 0.415 Round 4: 583 peptides, 97 chains. Longest chain 15 peptides. Score 0.423 Round 5: 604 peptides, 99 chains. Longest chain 16 peptides. Score 0.437 Taking the results from Round 5 Chains 102, Residues 505, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 23691 restraints for refining 10065 atoms. 21705 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1831 (Rfree = 0.000) for 10065 atoms. Found 44 (47 requested) and removed 90 (23 requested) atoms. Cycle 17: After refmac, R = 0.1701 (Rfree = 0.000) for 9970 atoms. Found 33 (47 requested) and removed 54 (23 requested) atoms. Cycle 18: After refmac, R = 0.1675 (Rfree = 0.000) for 9910 atoms. Found 26 (47 requested) and removed 46 (23 requested) atoms. Cycle 19: After refmac, R = 0.1667 (Rfree = 0.000) for 9867 atoms. Found 36 (46 requested) and removed 36 (23 requested) atoms. Cycle 20: After refmac, R = 0.1552 (Rfree = 0.000) for 9843 atoms. Found 24 (46 requested) and removed 37 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 4.14 Search for helices and strands: 0 residues in 0 chains, 10132 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 10150 seeds are put forward Round 1: 535 peptides, 108 chains. Longest chain 13 peptides. Score 0.307 Round 2: 569 peptides, 100 chains. Longest chain 12 peptides. Score 0.391 Round 3: 572 peptides, 99 chains. Longest chain 17 peptides. Score 0.400 Round 4: 600 peptides, 99 chains. Longest chain 16 peptides. Score 0.432 Round 5: 567 peptides, 100 chains. Longest chain 13 peptides. Score 0.389 Taking the results from Round 4 Chains 99, Residues 501, Estimated correctness of the model 0.0 % 9 chains (50 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 23501 restraints for refining 10086 atoms. 21460 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1818 (Rfree = 0.000) for 10086 atoms. Found 43 (47 requested) and removed 56 (23 requested) atoms. Cycle 22: After refmac, R = 0.1690 (Rfree = 0.000) for 10019 atoms. Found 39 (47 requested) and removed 58 (23 requested) atoms. Cycle 23: After refmac, R = 0.1694 (Rfree = 0.000) for 9969 atoms. Found 37 (47 requested) and removed 56 (23 requested) atoms. Cycle 24: After refmac, R = 0.1662 (Rfree = 0.000) for 9924 atoms. Found 47 (47 requested) and removed 46 (23 requested) atoms. Cycle 25: After refmac, R = 0.1648 (Rfree = 0.000) for 9900 atoms. Found 39 (47 requested) and removed 39 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 4.17 Search for helices and strands: 0 residues in 0 chains, 10199 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 10219 seeds are put forward Round 1: 461 peptides, 101 chains. Longest chain 10 peptides. Score 0.248 Round 2: 509 peptides, 96 chains. Longest chain 10 peptides. Score 0.338 Round 3: 528 peptides, 97 chains. Longest chain 13 peptides. Score 0.357 Round 4: 527 peptides, 95 chains. Longest chain 15 peptides. Score 0.366 Round 5: 507 peptides, 91 chains. Longest chain 13 peptides. Score 0.363 Taking the results from Round 4 Chains 95, Residues 432, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 24036 restraints for refining 10083 atoms. 22373 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1820 (Rfree = 0.000) for 10083 atoms. Found 47 (47 requested) and removed 62 (23 requested) atoms. Cycle 27: After refmac, R = 0.1918 (Rfree = 0.000) for 10011 atoms. Found 47 (47 requested) and removed 69 (23 requested) atoms. Cycle 28: After refmac, R = 0.1788 (Rfree = 0.000) for 9945 atoms. Found 45 (47 requested) and removed 38 (23 requested) atoms. Cycle 29: After refmac, R = 0.1920 (Rfree = 0.000) for 9925 atoms. Found 47 (47 requested) and removed 46 (23 requested) atoms. Cycle 30: After refmac, R = 0.1655 (Rfree = 0.000) for 9891 atoms. Found 47 (47 requested) and removed 45 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.87 4.19 Search for helices and strands: 0 residues in 0 chains, 10209 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 10220 seeds are put forward Round 1: 374 peptides, 84 chains. Longest chain 8 peptides. Score 0.224 Round 2: 478 peptides, 93 chains. Longest chain 12 peptides. Score 0.315 Round 3: 482 peptides, 86 chains. Longest chain 14 peptides. Score 0.358 Round 4: 492 peptides, 87 chains. Longest chain 15 peptides. Score 0.366 Round 5: 466 peptides, 81 chains. Longest chain 13 peptides. Score 0.366 Taking the results from Round 5 Chains 81, Residues 385, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 23589 restraints for refining 9855 atoms. 22069 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1839 (Rfree = 0.000) for 9855 atoms. Found 41 (46 requested) and removed 61 (23 requested) atoms. Cycle 32: After refmac, R = 0.1896 (Rfree = 0.000) for 9775 atoms. Found 46 (46 requested) and removed 46 (23 requested) atoms. Cycle 33: After refmac, R = 0.1816 (Rfree = 0.000) for 9752 atoms. Found 46 (46 requested) and removed 40 (23 requested) atoms. Cycle 34: After refmac, R = 0.1746 (Rfree = 0.000) for 9735 atoms. Found 46 (46 requested) and removed 41 (23 requested) atoms. Cycle 35: After refmac, R = 0.1711 (Rfree = 0.000) for 9724 atoms. Found 46 (46 requested) and removed 35 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.88 4.20 Search for helices and strands: 0 residues in 0 chains, 9947 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 9962 seeds are put forward Round 1: 358 peptides, 78 chains. Longest chain 10 peptides. Score 0.237 Round 2: 431 peptides, 86 chains. Longest chain 11 peptides. Score 0.292 Round 3: 418 peptides, 81 chains. Longest chain 11 peptides. Score 0.303 Round 4: 426 peptides, 77 chains. Longest chain 13 peptides. Score 0.337 Round 5: 419 peptides, 76 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 4 Chains 77, Residues 349, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 23051 restraints for refining 9635 atoms. 21719 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1748 (Rfree = 0.000) for 9635 atoms. Found 45 (45 requested) and removed 53 (22 requested) atoms. Cycle 37: After refmac, R = 0.1790 (Rfree = 0.000) for 9583 atoms. Found 45 (45 requested) and removed 50 (22 requested) atoms. Cycle 38: After refmac, R = 0.1671 (Rfree = 0.000) for 9551 atoms. Found 44 (45 requested) and removed 35 (22 requested) atoms. Cycle 39: After refmac, R = 0.1428 (Rfree = 0.000) for 9539 atoms. Found 23 (45 requested) and removed 33 (22 requested) atoms. Cycle 40: After refmac, R = 0.1680 (Rfree = 0.000) for 9515 atoms. Found 45 (45 requested) and removed 31 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 4.17 Search for helices and strands: 0 residues in 0 chains, 9797 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 9814 seeds are put forward Round 1: 329 peptides, 76 chains. Longest chain 8 peptides. Score 0.206 Round 2: 384 peptides, 80 chains. Longest chain 9 peptides. Score 0.262 Round 3: 387 peptides, 77 chains. Longest chain 10 peptides. Score 0.284 Round 4: 385 peptides, 76 chains. Longest chain 10 peptides. Score 0.287 Round 5: 398 peptides, 80 chains. Longest chain 10 peptides. Score 0.282 Taking the results from Round 4 Chains 76, Residues 309, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 23132 restraints for refining 9616 atoms. 21959 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1805 (Rfree = 0.000) for 9616 atoms. Found 45 (45 requested) and removed 76 (22 requested) atoms. Cycle 42: After refmac, R = 0.1817 (Rfree = 0.000) for 9544 atoms. Found 45 (45 requested) and removed 42 (22 requested) atoms. Cycle 43: After refmac, R = 0.1772 (Rfree = 0.000) for 9519 atoms. Found 45 (45 requested) and removed 34 (22 requested) atoms. Cycle 44: After refmac, R = 0.1302 (Rfree = 0.000) for 9508 atoms. Found 13 (45 requested) and removed 29 (22 requested) atoms. Cycle 45: After refmac, R = 0.1088 (Rfree = 0.000) for 9486 atoms. Found 12 (45 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.86 4.18 Search for helices and strands: 0 residues in 0 chains, 9702 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 9705 seeds are put forward Round 1: 311 peptides, 70 chains. Longest chain 7 peptides. Score 0.216 Round 2: 405 peptides, 83 chains. Longest chain 10 peptides. Score 0.274 Round 3: 392 peptides, 78 chains. Longest chain 9 peptides. Score 0.285 Round 4: 390 peptides, 76 chains. Longest chain 11 peptides. Score 0.294 Round 5: 381 peptides, 70 chains. Longest chain 11 peptides. Score 0.317 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 311, Estimated correctness of the model 0.0 % 4 chains (13 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2obn-4_warpNtrace.pdb as input Building loops using Loopy2018 70 chains (311 residues) following loop building 4 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11286 reflections ( 99.58 % complete ) and 22866 restraints for refining 9563 atoms. 21658 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1512 (Rfree = 0.000) for 9563 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.1694 (Rfree = 0.000) for 9514 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.1689 (Rfree = 0.000) for 9476 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.1766 (Rfree = 0.000) for 9437 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:52:32 GMT 2018 Job finished. TimeTaking 144.6 Used memory is bytes: 9360128