Mon 24 Dec 07:31:55 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 1vkz-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-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/1vkz-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-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 07:31:59 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/1vkz-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.4-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 683 and 0 Target number of residues in the AU: 683 Target solvent content: 0.5635 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-3.4-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: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.55 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: 19.959 3.400 Wilson plot Bfac: 39.52 11256 reflections ( 96.76 % complete ) and 0 restraints for refining 7267 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.2920 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2858 (Rfree = 0.000) for 7267 atoms. Found 54 (54 requested) and removed 106 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.83 2.95 Search for helices and strands: 0 residues in 0 chains, 7352 seeds are put forward NCS extension: 0 residues added, 7352 seeds are put forward Round 1: 297 peptides, 61 chains. Longest chain 9 peptides. Score 0.286 Round 2: 411 peptides, 67 chains. Longest chain 13 peptides. Score 0.457 Round 3: 469 peptides, 74 chains. Longest chain 15 peptides. Score 0.503 Round 4: 456 peptides, 68 chains. Longest chain 17 peptides. Score 0.524 Round 5: 486 peptides, 62 chains. Longest chain 22 peptides. Score 0.608 Taking the results from Round 5 Chains 64, Residues 424, Estimated correctness of the model 31.3 % 8 chains (64 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12573 restraints for refining 5993 atoms. 10721 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2590 (Rfree = 0.000) for 5993 atoms. Found 45 (45 requested) and removed 55 (22 requested) atoms. Cycle 2: After refmac, R = 0.2565 (Rfree = 0.000) for 5868 atoms. Found 45 (45 requested) and removed 46 (22 requested) atoms. Cycle 3: After refmac, R = 0.2195 (Rfree = 0.000) for 5813 atoms. Found 34 (44 requested) and removed 35 (22 requested) atoms. Cycle 4: After refmac, R = 0.2059 (Rfree = 0.000) for 5790 atoms. Found 28 (43 requested) and removed 31 (21 requested) atoms. Cycle 5: After refmac, R = 0.2016 (Rfree = 0.000) for 5760 atoms. Found 15 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.88 3.00 Search for helices and strands: 0 residues in 0 chains, 5907 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 5922 seeds are put forward Round 1: 445 peptides, 74 chains. Longest chain 16 peptides. Score 0.463 Round 2: 523 peptides, 69 chains. Longest chain 24 peptides. Score 0.616 Round 3: 520 peptides, 67 chains. Longest chain 23 peptides. Score 0.624 Round 4: 538 peptides, 70 chains. Longest chain 21 peptides. Score 0.630 Round 5: 514 peptides, 68 chains. Longest chain 21 peptides. Score 0.610 Taking the results from Round 4 Chains 75, Residues 468, Estimated correctness of the model 38.2 % 10 chains (69 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12362 restraints for refining 5878 atoms. 10345 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2357 (Rfree = 0.000) for 5878 atoms. Found 44 (44 requested) and removed 56 (22 requested) atoms. Cycle 7: After refmac, R = 0.2281 (Rfree = 0.000) for 5825 atoms. Found 41 (44 requested) and removed 46 (22 requested) atoms. Cycle 8: After refmac, R = 0.2110 (Rfree = 0.000) for 5780 atoms. Found 32 (43 requested) and removed 31 (21 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2112 (Rfree = 0.000) for 5769 atoms. Found 36 (43 requested) and removed 32 (21 requested) atoms. Cycle 10: After refmac, R = 0.1937 (Rfree = 0.000) for 5764 atoms. Found 16 (43 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.93 3.05 Search for helices and strands: 0 residues in 0 chains, 5919 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 5942 seeds are put forward Round 1: 440 peptides, 71 chains. Longest chain 18 peptides. Score 0.477 Round 2: 481 peptides, 69 chains. Longest chain 23 peptides. Score 0.556 Round 3: 509 peptides, 66 chains. Longest chain 33 peptides. Score 0.615 Round 4: 496 peptides, 68 chains. Longest chain 35 peptides. Score 0.585 Round 5: 523 peptides, 69 chains. Longest chain 33 peptides. Score 0.616 Taking the results from Round 5 Chains 72, Residues 454, Estimated correctness of the model 33.8 % 11 chains (76 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12557 restraints for refining 5994 atoms. 10554 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2718 (Rfree = 0.000) for 5994 atoms. Found 45 (45 requested) and removed 66 (22 requested) atoms. Cycle 12: After refmac, R = 0.2132 (Rfree = 0.000) for 5908 atoms. Found 34 (45 requested) and removed 42 (22 requested) atoms. Cycle 13: After refmac, R = 0.2059 (Rfree = 0.000) for 5873 atoms. Found 38 (44 requested) and removed 36 (22 requested) atoms. Cycle 14: After refmac, R = 0.1936 (Rfree = 0.000) for 5857 atoms. Found 26 (44 requested) and removed 30 (22 requested) atoms. Cycle 15: After refmac, R = 0.1847 (Rfree = 0.000) for 5843 atoms. Found 20 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.89 3.01 Search for helices and strands: 0 residues in 0 chains, 6001 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6019 seeds are put forward Round 1: 416 peptides, 67 chains. Longest chain 19 peptides. Score 0.465 Round 2: 476 peptides, 64 chains. Longest chain 19 peptides. Score 0.582 Round 3: 493 peptides, 64 chains. Longest chain 21 peptides. Score 0.606 Round 4: 483 peptides, 59 chains. Longest chain 25 peptides. Score 0.622 Round 5: 469 peptides, 61 chains. Longest chain 23 peptides. Score 0.591 Taking the results from Round 4 Chains 64, Residues 424, Estimated correctness of the model 35.7 % 5 chains (49 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12836 restraints for refining 5994 atoms. 11008 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2304 (Rfree = 0.000) for 5994 atoms. Found 38 (45 requested) and removed 42 (22 requested) atoms. Cycle 17: After refmac, R = 0.2052 (Rfree = 0.000) for 5959 atoms. Found 27 (45 requested) and removed 40 (22 requested) atoms. Cycle 18: After refmac, R = 0.1981 (Rfree = 0.000) for 5929 atoms. Found 20 (44 requested) and removed 32 (22 requested) atoms. Cycle 19: After refmac, R = 0.1908 (Rfree = 0.000) for 5906 atoms. Found 26 (44 requested) and removed 28 (22 requested) atoms. Cycle 20: After refmac, R = 0.1876 (Rfree = 0.000) for 5891 atoms. Found 19 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.91 3.03 Search for helices and strands: 0 residues in 0 chains, 6052 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6069 seeds are put forward Round 1: 414 peptides, 71 chains. Longest chain 16 peptides. Score 0.431 Round 2: 458 peptides, 71 chains. Longest chain 20 peptides. Score 0.507 Round 3: 484 peptides, 67 chains. Longest chain 26 peptides. Score 0.574 Round 4: 479 peptides, 69 chains. Longest chain 18 peptides. Score 0.553 Round 5: 463 peptides, 66 chains. Longest chain 26 peptides. Score 0.549 Taking the results from Round 3 Chains 72, Residues 417, Estimated correctness of the model 20.0 % 7 chains (66 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12374 restraints for refining 5994 atoms. 10546 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2175 (Rfree = 0.000) for 5994 atoms. Found 45 (45 requested) and removed 46 (22 requested) atoms. Cycle 22: After refmac, R = 0.2045 (Rfree = 0.000) for 5964 atoms. Found 35 (45 requested) and removed 28 (22 requested) atoms. Cycle 23: After refmac, R = 0.1948 (Rfree = 0.000) for 5946 atoms. Found 27 (45 requested) and removed 28 (22 requested) atoms. Cycle 24: After refmac, R = 0.1839 (Rfree = 0.000) for 5928 atoms. Found 21 (44 requested) and removed 31 (22 requested) atoms. Cycle 25: After refmac, R = 0.1804 (Rfree = 0.000) for 5903 atoms. Found 20 (44 requested) and removed 32 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.86 2.98 Search for helices and strands: 0 residues in 0 chains, 6057 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 6091 seeds are put forward Round 1: 430 peptides, 74 chains. Longest chain 15 peptides. Score 0.437 Round 2: 461 peptides, 70 chains. Longest chain 23 peptides. Score 0.518 Round 3: 465 peptides, 71 chains. Longest chain 24 peptides. Score 0.518 Round 4: 478 peptides, 68 chains. Longest chain 18 peptides. Score 0.558 Round 5: 460 peptides, 63 chains. Longest chain 32 peptides. Score 0.565 Taking the results from Round 5 Chains 67, Residues 397, Estimated correctness of the model 16.8 % 6 chains (61 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12770 restraints for refining 5994 atoms. 11046 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2198 (Rfree = 0.000) for 5994 atoms. Found 45 (45 requested) and removed 45 (22 requested) atoms. Cycle 27: After refmac, R = 0.2011 (Rfree = 0.000) for 5958 atoms. Found 37 (45 requested) and removed 29 (22 requested) atoms. Cycle 28: After refmac, R = 0.1897 (Rfree = 0.000) for 5942 atoms. Found 32 (45 requested) and removed 26 (22 requested) atoms. Cycle 29: After refmac, R = 0.1783 (Rfree = 0.000) for 5936 atoms. Found 29 (44 requested) and removed 30 (22 requested) atoms. Cycle 30: After refmac, R = 0.1707 (Rfree = 0.000) for 5929 atoms. Found 24 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.91 3.03 Search for helices and strands: 0 residues in 0 chains, 6099 seeds are put forward NCS extension: 26 residues added (9 deleted due to clashes), 6125 seeds are put forward Round 1: 364 peptides, 64 chains. Longest chain 17 peptides. Score 0.394 Round 2: 425 peptides, 61 chains. Longest chain 26 peptides. Score 0.524 Round 3: 429 peptides, 59 chains. Longest chain 20 peptides. Score 0.544 Round 4: 431 peptides, 58 chains. Longest chain 19 peptides. Score 0.554 Round 5: 434 peptides, 62 chains. Longest chain 21 peptides. Score 0.531 Taking the results from Round 4 Chains 62, Residues 373, Estimated correctness of the model 13.0 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 13111 restraints for refining 5994 atoms. 11565 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1959 (Rfree = 0.000) for 5994 atoms. Found 33 (45 requested) and removed 39 (22 requested) atoms. Cycle 32: After refmac, R = 0.1824 (Rfree = 0.000) for 5965 atoms. Found 25 (45 requested) and removed 26 (22 requested) atoms. Cycle 33: After refmac, R = 0.1771 (Rfree = 0.000) for 5950 atoms. Found 19 (45 requested) and removed 25 (22 requested) atoms. Cycle 34: After refmac, R = 0.1702 (Rfree = 0.000) for 5931 atoms. Found 18 (44 requested) and removed 26 (22 requested) atoms. Cycle 35: After refmac, R = 0.1622 (Rfree = 0.000) for 5918 atoms. Found 17 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.91 3.03 Search for helices and strands: 0 residues in 0 chains, 6047 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6066 seeds are put forward Round 1: 379 peptides, 66 chains. Longest chain 20 peptides. Score 0.407 Round 2: 418 peptides, 56 chains. Longest chain 19 peptides. Score 0.548 Round 3: 415 peptides, 59 chains. Longest chain 19 peptides. Score 0.522 Round 4: 413 peptides, 58 chains. Longest chain 17 peptides. Score 0.526 Round 5: 424 peptides, 62 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 2 Chains 61, Residues 362, Estimated correctness of the model 10.8 % 7 chains (66 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 12817 restraints for refining 5994 atoms. 11169 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1956 (Rfree = 0.000) for 5994 atoms. Found 32 (45 requested) and removed 42 (22 requested) atoms. Cycle 37: After refmac, R = 0.1860 (Rfree = 0.000) for 5968 atoms. Found 33 (45 requested) and removed 25 (22 requested) atoms. Cycle 38: After refmac, R = 0.1791 (Rfree = 0.000) for 5966 atoms. Found 29 (45 requested) and removed 29 (22 requested) atoms. Cycle 39: After refmac, R = 0.1689 (Rfree = 0.000) for 5961 atoms. Found 20 (45 requested) and removed 25 (22 requested) atoms. Cycle 40: After refmac, R = 0.1655 (Rfree = 0.000) for 5950 atoms. Found 14 (44 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.91 3.03 Search for helices and strands: 0 residues in 0 chains, 6051 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6066 seeds are put forward Round 1: 341 peptides, 59 chains. Longest chain 19 peptides. Score 0.392 Round 2: 381 peptides, 59 chains. Longest chain 23 peptides. Score 0.465 Round 3: 373 peptides, 57 chains. Longest chain 21 peptides. Score 0.466 Round 4: 382 peptides, 57 chains. Longest chain 21 peptides. Score 0.482 Round 5: 378 peptides, 54 chains. Longest chain 22 peptides. Score 0.498 Taking the results from Round 5 Chains 55, Residues 324, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 11256 reflections ( 96.76 % complete ) and 13589 restraints for refining 5994 atoms. 12200 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2000 (Rfree = 0.000) for 5994 atoms. Found 43 (45 requested) and removed 33 (22 requested) atoms. Cycle 42: After refmac, R = 0.1857 (Rfree = 0.000) for 5986 atoms. Found 28 (45 requested) and removed 26 (22 requested) atoms. Cycle 43: After refmac, R = 0.1756 (Rfree = 0.000) for 5974 atoms. Found 24 (45 requested) and removed 27 (22 requested) atoms. Cycle 44: After refmac, R = 0.1726 (Rfree = 0.000) for 5962 atoms. Found 23 (45 requested) and removed 26 (22 requested) atoms. Cycle 45: After refmac, R = 0.1692 (Rfree = 0.000) for 5950 atoms. Found 24 (44 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.88 3.00 Search for helices and strands: 0 residues in 0 chains, 6066 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 6089 seeds are put forward Round 1: 314 peptides, 57 chains. Longest chain 17 peptides. Score 0.356 Round 2: 356 peptides, 56 chains. Longest chain 19 peptides. Score 0.444 Round 3: 361 peptides, 55 chains. Longest chain 17 peptides. Score 0.461 Round 4: 349 peptides, 57 chains. Longest chain 16 peptides. Score 0.423 Round 5: 365 peptides, 54 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 311, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 56 chains (311 residues) following loop building 4 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11256 reflections ( 96.76 % complete ) and 13429 restraints for refining 5994 atoms. 12127 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2068 (Rfree = 0.000) for 5994 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.1879 (Rfree = 0.000) for 5948 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.1780 (Rfree = 0.000) for 5913 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.1704 (Rfree = 0.000) for 5888 atoms. TimeTaking 56.45