null Sun 23 Dec 22:22:43 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 1vqy-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.6-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/1vqy-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.6-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 22:22:52 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/1vqy-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.6-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 754 and 0 Target number of residues in the AU: 754 Target solvent content: 0.5834 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-3.6-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: 19 Cell parameters: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 7424 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: 29.074 3.600 Wilson plot Bfac: 46.12 11704 reflections ( 98.35 % complete ) and 0 restraints for refining 8233 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.2826 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2815 (Rfree = 0.000) for 8233 atoms. Found 52 (52 requested) and removed 63 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.08 Search for helices and strands: 0 residues in 0 chains, 8378 seeds are put forward NCS extension: 0 residues added, 8378 seeds are put forward Round 1: 403 peptides, 76 chains. Longest chain 14 peptides. Score 0.350 Round 2: 520 peptides, 78 chains. Longest chain 17 peptides. Score 0.518 Round 3: 568 peptides, 78 chains. Longest chain 26 peptides. Score 0.581 Round 4: 576 peptides, 74 chains. Longest chain 21 peptides. Score 0.613 Round 5: 564 peptides, 69 chains. Longest chain 23 peptides. Score 0.625 Taking the results from Round 5 Chains 69, Residues 495, Estimated correctness of the model 24.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 15034 restraints for refining 6727 atoms. 13123 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2324 (Rfree = 0.000) for 6727 atoms. Found 30 (43 requested) and removed 54 (21 requested) atoms. Cycle 2: After refmac, R = 0.2188 (Rfree = 0.000) for 6637 atoms. Found 20 (43 requested) and removed 53 (21 requested) atoms. Cycle 3: After refmac, R = 0.2051 (Rfree = 0.000) for 6577 atoms. Found 27 (42 requested) and removed 39 (21 requested) atoms. Cycle 4: After refmac, R = 0.1933 (Rfree = 0.000) for 6547 atoms. Found 20 (42 requested) and removed 37 (21 requested) atoms. Cycle 5: After refmac, R = 0.1906 (Rfree = 0.000) for 6514 atoms. Found 22 (41 requested) and removed 31 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 6753 seeds are put forward NCS extension: 12 residues added (7 deleted due to clashes), 6765 seeds are put forward Round 1: 468 peptides, 75 chains. Longest chain 22 peptides. Score 0.462 Round 2: 532 peptides, 71 chains. Longest chain 22 peptides. Score 0.575 Round 3: 575 peptides, 71 chains. Longest chain 31 peptides. Score 0.627 Round 4: 552 peptides, 67 chains. Longest chain 29 peptides. Score 0.621 Round 5: 562 peptides, 67 chains. Longest chain 23 peptides. Score 0.633 Taking the results from Round 5 Chains 68, Residues 495, Estimated correctness of the model 27.1 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 14765 restraints for refining 6730 atoms. 12716 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2229 (Rfree = 0.000) for 6730 atoms. Found 39 (43 requested) and removed 51 (21 requested) atoms. Cycle 7: After refmac, R = 0.2073 (Rfree = 0.000) for 6695 atoms. Found 19 (43 requested) and removed 53 (21 requested) atoms. Cycle 8: After refmac, R = 0.1986 (Rfree = 0.000) for 6636 atoms. Found 22 (42 requested) and removed 44 (21 requested) atoms. Cycle 9: After refmac, R = 0.1888 (Rfree = 0.000) for 6611 atoms. Found 17 (42 requested) and removed 43 (21 requested) atoms. Cycle 10: After refmac, R = 0.1841 (Rfree = 0.000) for 6578 atoms. Found 18 (42 requested) and removed 38 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.13 Search for helices and strands: 0 residues in 0 chains, 6794 seeds are put forward NCS extension: 12 residues added (7 deleted due to clashes), 6806 seeds are put forward Round 1: 471 peptides, 69 chains. Longest chain 18 peptides. Score 0.505 Round 2: 536 peptides, 70 chains. Longest chain 20 peptides. Score 0.586 Round 3: 542 peptides, 69 chains. Longest chain 21 peptides. Score 0.599 Round 4: 540 peptides, 61 chains. Longest chain 24 peptides. Score 0.639 Round 5: 518 peptides, 60 chains. Longest chain 25 peptides. Score 0.619 Taking the results from Round 4 Chains 64, Residues 479, Estimated correctness of the model 29.3 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 14591 restraints for refining 6729 atoms. 12550 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2117 (Rfree = 0.000) for 6729 atoms. Found 37 (43 requested) and removed 50 (21 requested) atoms. Cycle 12: After refmac, R = 0.2041 (Rfree = 0.000) for 6686 atoms. Found 35 (43 requested) and removed 35 (21 requested) atoms. Cycle 13: After refmac, R = 0.1996 (Rfree = 0.000) for 6667 atoms. Found 38 (42 requested) and removed 32 (21 requested) atoms. Cycle 14: After refmac, R = 0.1971 (Rfree = 0.000) for 6663 atoms. Found 24 (42 requested) and removed 36 (21 requested) atoms. Cycle 15: After refmac, R = 0.1915 (Rfree = 0.000) for 6637 atoms. Found 30 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 3.08 Search for helices and strands: 0 residues in 0 chains, 6857 seeds are put forward NCS extension: 19 residues added (9 deleted due to clashes), 6876 seeds are put forward Round 1: 475 peptides, 77 chains. Longest chain 13 peptides. Score 0.459 Round 2: 543 peptides, 72 chains. Longest chain 22 peptides. Score 0.583 Round 3: 522 peptides, 70 chains. Longest chain 21 peptides. Score 0.568 Round 4: 522 peptides, 71 chains. Longest chain 22 peptides. Score 0.562 Round 5: 528 peptides, 71 chains. Longest chain 22 peptides. Score 0.570 Taking the results from Round 2 Chains 75, Residues 471, Estimated correctness of the model 7.9 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 14850 restraints for refining 6730 atoms. 12931 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2108 (Rfree = 0.000) for 6730 atoms. Found 30 (43 requested) and removed 44 (21 requested) atoms. Cycle 17: After refmac, R = 0.2069 (Rfree = 0.000) for 6700 atoms. Found 22 (43 requested) and removed 40 (21 requested) atoms. Cycle 18: After refmac, R = 0.2048 (Rfree = 0.000) for 6666 atoms. Found 25 (42 requested) and removed 37 (21 requested) atoms. Cycle 19: After refmac, R = 0.1955 (Rfree = 0.000) for 6647 atoms. Found 21 (42 requested) and removed 40 (21 requested) atoms. Cycle 20: After refmac, R = 0.1924 (Rfree = 0.000) for 6622 atoms. Found 17 (42 requested) and removed 36 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 3.09 Search for helices and strands: 0 residues in 0 chains, 6856 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 6890 seeds are put forward Round 1: 462 peptides, 74 chains. Longest chain 22 peptides. Score 0.459 Round 2: 500 peptides, 70 chains. Longest chain 20 peptides. Score 0.539 Round 3: 493 peptides, 66 chains. Longest chain 24 peptides. Score 0.554 Round 4: 508 peptides, 70 chains. Longest chain 30 peptides. Score 0.550 Round 5: 525 peptides, 72 chains. Longest chain 29 peptides. Score 0.560 Taking the results from Round 5 Chains 74, Residues 453, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 15107 restraints for refining 6730 atoms. 13300 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2081 (Rfree = 0.000) for 6730 atoms. Found 33 (43 requested) and removed 44 (21 requested) atoms. Cycle 22: After refmac, R = 0.1991 (Rfree = 0.000) for 6702 atoms. Found 22 (43 requested) and removed 47 (21 requested) atoms. Cycle 23: After refmac, R = 0.1949 (Rfree = 0.000) for 6669 atoms. Found 22 (42 requested) and removed 34 (21 requested) atoms. Cycle 24: After refmac, R = 0.1889 (Rfree = 0.000) for 6650 atoms. Found 19 (42 requested) and removed 33 (21 requested) atoms. Cycle 25: After refmac, R = 0.1854 (Rfree = 0.000) for 6626 atoms. Found 18 (42 requested) and removed 30 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.12 Search for helices and strands: 0 residues in 0 chains, 6836 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 6848 seeds are put forward Round 1: 428 peptides, 77 chains. Longest chain 11 peptides. Score 0.385 Round 2: 459 peptides, 67 chains. Longest chain 15 peptides. Score 0.500 Round 3: 483 peptides, 68 chains. Longest chain 18 peptides. Score 0.528 Round 4: 493 peptides, 64 chains. Longest chain 31 peptides. Score 0.565 Round 5: 496 peptides, 70 chains. Longest chain 20 peptides. Score 0.534 Taking the results from Round 4 Chains 66, Residues 429, Estimated correctness of the model 0.5 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 14903 restraints for refining 6730 atoms. 13130 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2080 (Rfree = 0.000) for 6730 atoms. Found 38 (43 requested) and removed 36 (21 requested) atoms. Cycle 27: After refmac, R = 0.2150 (Rfree = 0.000) for 6713 atoms. Found 43 (43 requested) and removed 41 (21 requested) atoms. Cycle 28: After refmac, R = 0.2037 (Rfree = 0.000) for 6699 atoms. Found 31 (43 requested) and removed 35 (21 requested) atoms. Cycle 29: After refmac, R = 0.1790 (Rfree = 0.000) for 6681 atoms. Found 8 (42 requested) and removed 24 (21 requested) atoms. Cycle 30: After refmac, R = 0.1762 (Rfree = 0.000) for 6660 atoms. Found 11 (42 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 6898 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 6926 seeds are put forward Round 1: 453 peptides, 81 chains. Longest chain 14 peptides. Score 0.398 Round 2: 479 peptides, 69 chains. Longest chain 19 peptides. Score 0.516 Round 3: 492 peptides, 68 chains. Longest chain 18 peptides. Score 0.540 Round 4: 489 peptides, 73 chains. Longest chain 16 peptides. Score 0.505 Round 5: 485 peptides, 66 chains. Longest chain 27 peptides. Score 0.543 Taking the results from Round 5 Chains 67, Residues 419, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 15134 restraints for refining 6729 atoms. 13467 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2159 (Rfree = 0.000) for 6729 atoms. Found 35 (43 requested) and removed 44 (21 requested) atoms. Cycle 32: After refmac, R = 0.2130 (Rfree = 0.000) for 6701 atoms. Found 29 (43 requested) and removed 46 (21 requested) atoms. Cycle 33: After refmac, R = 0.2054 (Rfree = 0.000) for 6671 atoms. Found 30 (42 requested) and removed 34 (21 requested) atoms. Cycle 34: After refmac, R = 0.2059 (Rfree = 0.000) for 6662 atoms. Found 28 (42 requested) and removed 39 (21 requested) atoms. Cycle 35: After refmac, R = 0.2036 (Rfree = 0.000) for 6648 atoms. Found 30 (42 requested) and removed 45 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 3.07 Search for helices and strands: 0 residues in 0 chains, 6818 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6842 seeds are put forward Round 1: 367 peptides, 72 chains. Longest chain 12 peptides. Score 0.317 Round 2: 422 peptides, 69 chains. Longest chain 13 peptides. Score 0.431 Round 3: 406 peptides, 62 chains. Longest chain 13 peptides. Score 0.454 Round 4: 412 peptides, 63 chains. Longest chain 13 peptides. Score 0.456 Round 5: 422 peptides, 62 chains. Longest chain 16 peptides. Score 0.478 Taking the results from Round 5 Chains 62, Residues 360, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 15950 restraints for refining 6730 atoms. 14572 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2069 (Rfree = 0.000) for 6730 atoms. Found 26 (43 requested) and removed 30 (21 requested) atoms. Cycle 37: After refmac, R = 0.2113 (Rfree = 0.000) for 6717 atoms. Found 43 (43 requested) and removed 28 (21 requested) atoms. Cycle 38: After refmac, R = 0.2051 (Rfree = 0.000) for 6720 atoms. Found 43 (43 requested) and removed 38 (21 requested) atoms. Cycle 39: After refmac, R = 0.1758 (Rfree = 0.000) for 6721 atoms. Found 13 (43 requested) and removed 27 (21 requested) atoms. Cycle 40: After refmac, R = 0.1687 (Rfree = 0.000) for 6703 atoms. Found 5 (43 requested) and removed 26 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 6878 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 6893 seeds are put forward Round 1: 350 peptides, 67 chains. Longest chain 15 peptides. Score 0.324 Round 2: 383 peptides, 59 chains. Longest chain 16 peptides. Score 0.439 Round 3: 392 peptides, 60 chains. Longest chain 17 peptides. Score 0.446 Round 4: 379 peptides, 55 chains. Longest chain 17 peptides. Score 0.460 Round 5: 407 peptides, 60 chains. Longest chain 17 peptides. Score 0.469 Taking the results from Round 5 Chains 61, Residues 347, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 11704 reflections ( 98.35 % complete ) and 15736 restraints for refining 6729 atoms. 14373 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1974 (Rfree = 0.000) for 6729 atoms. Found 30 (43 requested) and removed 29 (21 requested) atoms. Cycle 42: After refmac, R = 0.1943 (Rfree = 0.000) for 6713 atoms. Found 36 (43 requested) and removed 25 (21 requested) atoms. Cycle 43: After refmac, R = 0.1922 (Rfree = 0.000) for 6711 atoms. Found 43 (43 requested) and removed 31 (21 requested) atoms. Cycle 44: After refmac, R = 0.1948 (Rfree = 0.000) for 6718 atoms. Found 43 (43 requested) and removed 24 (21 requested) atoms. Cycle 45: After refmac, R = 0.1917 (Rfree = 0.000) for 6731 atoms. Found 43 (43 requested) and removed 35 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.06 3.10 Search for helices and strands: 0 residues in 0 chains, 6920 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 6942 seeds are put forward Round 1: 329 peptides, 60 chains. Longest chain 18 peptides. Score 0.340 Round 2: 372 peptides, 60 chains. Longest chain 15 peptides. Score 0.414 Round 3: 379 peptides, 64 chains. Longest chain 13 peptides. Score 0.397 Round 4: 385 peptides, 58 chains. Longest chain 19 peptides. Score 0.449 Round 5: 377 peptides, 59 chains. Longest chain 15 peptides. Score 0.429 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 327, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vqy-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11704 reflections ( 98.35 % complete ) and 16086 restraints for refining 6730 atoms. 14836 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2014 (Rfree = 0.000) for 6730 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.2105 (Rfree = 0.000) for 6694 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2101 (Rfree = 0.000) for 6667 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2077 (Rfree = 0.000) for 6642 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:49:52 GMT 2018 Job finished. TimeTaking 87.15 Used memory is bytes: 10614648