null Tue 25 Dec 19:27:57 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 2ash-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ash-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ash-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-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/2ash-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-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 19:28:07 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/2ash-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-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 1052 and 0 Target number of residues in the AU: 1052 Target solvent content: 0.6761 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.85 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: 103.605 4.000 Wilson plot Bfac: 97.66 14751 reflections ( 99.68 % complete ) and 0 restraints for refining 13501 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3427 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3402 (Rfree = 0.000) for 13501 atoms. Found 64 (64 requested) and removed 205 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.68 Search for helices and strands: 0 residues in 0 chains, 13564 seeds are put forward NCS extension: 0 residues added, 13564 seeds are put forward Round 1: 412 peptides, 86 chains. Longest chain 14 peptides. Score 0.250 Round 2: 555 peptides, 102 chains. Longest chain 14 peptides. Score 0.329 Round 3: 608 peptides, 106 chains. Longest chain 16 peptides. Score 0.365 Round 4: 638 peptides, 106 chains. Longest chain 14 peptides. Score 0.393 Round 5: 630 peptides, 100 chains. Longest chain 20 peptides. Score 0.410 Taking the results from Round 5 Chains 100, Residues 530, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 26960 restraints for refining 11007 atoms. 24912 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2707 (Rfree = 0.000) for 11007 atoms. Found 52 (52 requested) and removed 88 (26 requested) atoms. Cycle 2: After refmac, R = 0.2616 (Rfree = 0.000) for 10816 atoms. Found 52 (52 requested) and removed 77 (26 requested) atoms. Cycle 3: After refmac, R = 0.2394 (Rfree = 0.000) for 10697 atoms. Found 35 (51 requested) and removed 48 (25 requested) atoms. Cycle 4: After refmac, R = 0.2455 (Rfree = 0.000) for 10595 atoms. Found 50 (50 requested) and removed 58 (25 requested) atoms. Cycle 5: After refmac, R = 0.2343 (Rfree = 0.000) for 10525 atoms. Found 50 (50 requested) and removed 47 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.67 Search for helices and strands: 0 residues in 0 chains, 10853 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10872 seeds are put forward Round 1: 553 peptides, 108 chains. Longest chain 10 peptides. Score 0.301 Round 2: 684 peptides, 115 chains. Longest chain 16 peptides. Score 0.399 Round 3: 704 peptides, 110 chains. Longest chain 20 peptides. Score 0.437 Round 4: 690 peptides, 107 chains. Longest chain 17 peptides. Score 0.437 Round 5: 702 peptides, 104 chains. Longest chain 17 peptides. Score 0.459 Taking the results from Round 5 Chains 108, Residues 598, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 24650 restraints for refining 10622 atoms. 22265 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2239 (Rfree = 0.000) for 10622 atoms. Found 44 (50 requested) and removed 100 (25 requested) atoms. Cycle 7: After refmac, R = 0.2204 (Rfree = 0.000) for 10463 atoms. Found 46 (50 requested) and removed 77 (25 requested) atoms. Cycle 8: After refmac, R = 0.1762 (Rfree = 0.000) for 10370 atoms. Found 12 (49 requested) and removed 38 (24 requested) atoms. Cycle 9: After refmac, R = 0.1658 (Rfree = 0.000) for 10302 atoms. Found 8 (49 requested) and removed 30 (24 requested) atoms. Cycle 10: After refmac, R = 0.1632 (Rfree = 0.000) for 10263 atoms. Found 11 (48 requested) and removed 38 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 10572 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 10592 seeds are put forward Round 1: 626 peptides, 121 chains. Longest chain 10 peptides. Score 0.319 Round 2: 682 peptides, 111 chains. Longest chain 15 peptides. Score 0.414 Round 3: 710 peptides, 105 chains. Longest chain 19 peptides. Score 0.462 Round 4: 720 peptides, 108 chains. Longest chain 20 peptides. Score 0.459 Round 5: 710 peptides, 110 chains. Longest chain 19 peptides. Score 0.443 Taking the results from Round 3 Chains 105, Residues 605, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 24742 restraints for refining 10687 atoms. 22411 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2247 (Rfree = 0.000) for 10687 atoms. Found 50 (50 requested) and removed 107 (25 requested) atoms. Cycle 12: After refmac, R = 0.2196 (Rfree = 0.000) for 10540 atoms. Found 50 (50 requested) and removed 67 (25 requested) atoms. Cycle 13: After refmac, R = 0.2083 (Rfree = 0.000) for 10446 atoms. Found 49 (49 requested) and removed 64 (24 requested) atoms. Cycle 14: After refmac, R = 0.1999 (Rfree = 0.000) for 10374 atoms. Found 49 (49 requested) and removed 42 (24 requested) atoms. Cycle 15: After refmac, R = 0.1988 (Rfree = 0.000) for 10332 atoms. Found 49 (49 requested) and removed 53 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 10734 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 10759 seeds are put forward Round 1: 562 peptides, 106 chains. Longest chain 12 peptides. Score 0.319 Round 2: 643 peptides, 102 chains. Longest chain 19 peptides. Score 0.414 Round 3: 652 peptides, 102 chains. Longest chain 17 peptides. Score 0.422 Round 4: 668 peptides, 103 chains. Longest chain 20 peptides. Score 0.433 Round 5: 686 peptides, 110 chains. Longest chain 17 peptides. Score 0.421 Taking the results from Round 4 Chains 103, Residues 565, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 24743 restraints for refining 10780 atoms. 22580 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2097 (Rfree = 0.000) for 10780 atoms. Found 51 (51 requested) and removed 81 (25 requested) atoms. Cycle 17: After refmac, R = 0.2161 (Rfree = 0.000) for 10673 atoms. Found 51 (51 requested) and removed 59 (25 requested) atoms. Cycle 18: After refmac, R = 0.1949 (Rfree = 0.000) for 10606 atoms. Found 50 (50 requested) and removed 50 (25 requested) atoms. Cycle 19: After refmac, R = 0.1985 (Rfree = 0.000) for 10570 atoms. Found 50 (50 requested) and removed 49 (25 requested) atoms. Cycle 20: After refmac, R = 0.1852 (Rfree = 0.000) for 10533 atoms. Found 50 (50 requested) and removed 42 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 10908 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 10933 seeds are put forward Round 1: 539 peptides, 107 chains. Longest chain 11 peptides. Score 0.291 Round 2: 624 peptides, 104 chains. Longest chain 19 peptides. Score 0.388 Round 3: 626 peptides, 98 chains. Longest chain 14 peptides. Score 0.415 Round 4: 632 peptides, 94 chains. Longest chain 18 peptides. Score 0.436 Round 5: 644 peptides, 100 chains. Longest chain 20 peptides. Score 0.423 Taking the results from Round 4 Chains 94, Residues 538, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 25742 restraints for refining 10951 atoms. 23652 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2203 (Rfree = 0.000) for 10951 atoms. Found 52 (52 requested) and removed 75 (26 requested) atoms. Cycle 22: After refmac, R = 0.2110 (Rfree = 0.000) for 10853 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. Cycle 23: After refmac, R = 0.2037 (Rfree = 0.000) for 10800 atoms. Found 51 (51 requested) and removed 47 (25 requested) atoms. Cycle 24: After refmac, R = 0.1978 (Rfree = 0.000) for 10741 atoms. Found 51 (51 requested) and removed 41 (25 requested) atoms. Cycle 25: After refmac, R = 0.1993 (Rfree = 0.000) for 10707 atoms. Found 51 (51 requested) and removed 43 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 11062 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 11080 seeds are put forward Round 1: 507 peptides, 109 chains. Longest chain 9 peptides. Score 0.248 Round 2: 619 peptides, 112 chains. Longest chain 14 peptides. Score 0.350 Round 3: 619 peptides, 105 chains. Longest chain 14 peptides. Score 0.379 Round 4: 628 peptides, 102 chains. Longest chain 14 peptides. Score 0.400 Round 5: 652 peptides, 102 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 5 Chains 102, Residues 550, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 25850 restraints for refining 11008 atoms. 23752 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2076 (Rfree = 0.000) for 11008 atoms. Found 52 (52 requested) and removed 61 (26 requested) atoms. Cycle 27: After refmac, R = 0.2096 (Rfree = 0.000) for 10924 atoms. Found 52 (52 requested) and removed 60 (26 requested) atoms. Cycle 28: After refmac, R = 0.1948 (Rfree = 0.000) for 10858 atoms. Found 51 (51 requested) and removed 45 (25 requested) atoms. Cycle 29: After refmac, R = 0.1922 (Rfree = 0.000) for 10823 atoms. Found 51 (51 requested) and removed 40 (25 requested) atoms. Cycle 30: After refmac, R = 0.1887 (Rfree = 0.000) for 10792 atoms. Found 51 (51 requested) and removed 37 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 11134 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 11149 seeds are put forward Round 1: 504 peptides, 105 chains. Longest chain 15 peptides. Score 0.263 Round 2: 575 peptides, 104 chains. Longest chain 20 peptides. Score 0.341 Round 3: 605 peptides, 101 chains. Longest chain 18 peptides. Score 0.383 Round 4: 632 peptides, 109 chains. Longest chain 15 peptides. Score 0.375 Round 5: 623 peptides, 104 chains. Longest chain 14 peptides. Score 0.387 Taking the results from Round 5 Chains 104, Residues 519, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 26274 restraints for refining 11009 atoms. 24302 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2144 (Rfree = 0.000) for 11009 atoms. Found 52 (52 requested) and removed 68 (26 requested) atoms. Cycle 32: After refmac, R = 0.1986 (Rfree = 0.000) for 10907 atoms. Found 52 (52 requested) and removed 52 (26 requested) atoms. Cycle 33: After refmac, R = 0.1963 (Rfree = 0.000) for 10828 atoms. Found 51 (51 requested) and removed 51 (25 requested) atoms. Cycle 34: After refmac, R = 0.1960 (Rfree = 0.000) for 10778 atoms. Found 51 (51 requested) and removed 46 (25 requested) atoms. Cycle 35: After refmac, R = 0.1885 (Rfree = 0.000) for 10736 atoms. Found 51 (51 requested) and removed 39 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 11015 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 11030 seeds are put forward Round 1: 464 peptides, 96 chains. Longest chain 10 peptides. Score 0.260 Round 2: 540 peptides, 99 chains. Longest chain 13 peptides. Score 0.327 Round 3: 529 peptides, 87 chains. Longest chain 18 peptides. Score 0.369 Round 4: 548 peptides, 93 chains. Longest chain 14 peptides. Score 0.362 Round 5: 555 peptides, 91 chains. Longest chain 14 peptides. Score 0.377 Taking the results from Round 5 Chains 91, Residues 464, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 26559 restraints for refining 11010 atoms. 24794 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2188 (Rfree = 0.000) for 11010 atoms. Found 52 (52 requested) and removed 79 (26 requested) atoms. Cycle 37: After refmac, R = 0.2030 (Rfree = 0.000) for 10910 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. Cycle 38: After refmac, R = 0.1922 (Rfree = 0.000) for 10867 atoms. Found 51 (51 requested) and removed 52 (25 requested) atoms. Cycle 39: After refmac, R = 0.2010 (Rfree = 0.000) for 10814 atoms. Found 51 (51 requested) and removed 103 (25 requested) atoms. Cycle 40: After refmac, R = 0.1892 (Rfree = 0.000) for 10732 atoms. Found 51 (51 requested) and removed 56 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.90 3.75 Search for helices and strands: 0 residues in 0 chains, 11025 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11041 seeds are put forward Round 1: 448 peptides, 95 chains. Longest chain 9 peptides. Score 0.247 Round 2: 513 peptides, 98 chains. Longest chain 12 peptides. Score 0.304 Round 3: 516 peptides, 94 chains. Longest chain 11 peptides. Score 0.325 Round 4: 513 peptides, 94 chains. Longest chain 16 peptides. Score 0.322 Round 5: 500 peptides, 88 chains. Longest chain 14 peptides. Score 0.335 Taking the results from Round 5 Chains 88, Residues 412, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 25988 restraints for refining 10808 atoms. 24428 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2028 (Rfree = 0.000) for 10808 atoms. Found 51 (51 requested) and removed 47 (25 requested) atoms. Cycle 42: After refmac, R = 0.2039 (Rfree = 0.000) for 10764 atoms. Found 51 (51 requested) and removed 53 (25 requested) atoms. Cycle 43: After refmac, R = 0.2019 (Rfree = 0.000) for 10721 atoms. Found 51 (51 requested) and removed 42 (25 requested) atoms. Cycle 44: After refmac, R = 0.1978 (Rfree = 0.000) for 10687 atoms. Found 50 (50 requested) and removed 43 (25 requested) atoms. Cycle 45: After refmac, R = 0.1927 (Rfree = 0.000) for 10668 atoms. Found 50 (50 requested) and removed 35 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.90 3.75 Search for helices and strands: 0 residues in 0 chains, 10991 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 11009 seeds are put forward Round 1: 386 peptides, 84 chains. Longest chain 10 peptides. Score 0.229 Round 2: 460 peptides, 93 chains. Longest chain 11 peptides. Score 0.270 Round 3: 475 peptides, 86 chains. Longest chain 13 peptides. Score 0.319 Round 4: 513 peptides, 92 chains. Longest chain 12 peptides. Score 0.331 Round 5: 474 peptides, 86 chains. Longest chain 12 peptides. Score 0.318 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 93, Residues 421, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2ash-4_warpNtrace.pdb as input Building loops using Loopy2018 93 chains (421 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14751 reflections ( 99.68 % complete ) and 25325 restraints for refining 10683 atoms. 23694 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2171 (Rfree = 0.000) for 10683 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 47: After refmac, R = 0.2078 (Rfree = 0.000) for 10585 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 48: After refmac, R = 0.2226 (Rfree = 0.000) for 10514 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.1902 (Rfree = 0.000) for 10443 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:59:44 GMT 2018 Job finished. TimeTaking 151.78 Used memory is bytes: 14133904