null Mon 24 Dec 08:01:48 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 2anu-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2anu-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2anu-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-4.0-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/2anu-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-4.0-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 08:01:53 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/2anu-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-4.0-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 1242 and 0 Target number of residues in the AU: 1242 Target solvent content: 0.6319 Checking the provided sequence file Detected sequence length: 255 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1530 Adjusted target solvent content: 0.55 Input MTZ file: 2anu-4.0-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 12240 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: 127.729 4.001 Wilson plot Bfac: 67.56 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 14900 reflections ( 99.71 % complete ) and 0 restraints for refining 13566 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3050 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2931 (Rfree = 0.000) for 13566 atoms. Found 64 (64 requested) and removed 40 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 13790 seeds are put forward NCS extension: 0 residues added, 13790 seeds are put forward Round 1: 511 peptides, 101 chains. Longest chain 11 peptides. Score 0.285 Round 2: 701 peptides, 110 chains. Longest chain 21 peptides. Score 0.427 Round 3: 753 peptides, 110 chains. Longest chain 16 peptides. Score 0.471 Round 4: 756 peptides, 108 chains. Longest chain 19 peptides. Score 0.481 Round 5: 816 peptides, 114 chains. Longest chain 27 peptides. Score 0.507 Taking the results from Round 5 Chains 116, Residues 702, Estimated correctness of the model 0.0 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 25992 restraints for refining 11049 atoms. 23138 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2233 (Rfree = 0.000) for 11049 atoms. Found 41 (52 requested) and removed 51 (26 requested) atoms. Cycle 2: After refmac, R = 0.2058 (Rfree = 0.000) for 10865 atoms. Found 38 (52 requested) and removed 53 (26 requested) atoms. Cycle 3: After refmac, R = 0.2051 (Rfree = 0.000) for 10786 atoms. Found 51 (51 requested) and removed 43 (25 requested) atoms. Cycle 4: After refmac, R = 0.1736 (Rfree = 0.000) for 10752 atoms. Found 20 (51 requested) and removed 32 (25 requested) atoms. Cycle 5: After refmac, R = 0.1644 (Rfree = 0.000) for 10700 atoms. Found 18 (50 requested) and removed 36 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.32 Search for helices and strands: 0 residues in 0 chains, 11043 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 11074 seeds are put forward Round 1: 679 peptides, 121 chains. Longest chain 14 peptides. Score 0.365 Round 2: 766 peptides, 117 chains. Longest chain 21 peptides. Score 0.456 Round 3: 757 peptides, 108 chains. Longest chain 21 peptides. Score 0.482 Round 4: 771 peptides, 110 chains. Longest chain 18 peptides. Score 0.486 Round 5: 772 peptides, 108 chains. Longest chain 18 peptides. Score 0.494 Taking the results from Round 5 Chains 108, Residues 664, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26716 restraints for refining 11053 atoms. 24168 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2260 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 7: After refmac, R = 0.2139 (Rfree = 0.000) for 10903 atoms. Found 52 (52 requested) and removed 51 (26 requested) atoms. Cycle 8: After refmac, R = 0.1784 (Rfree = 0.000) for 10833 atoms. Found 24 (51 requested) and removed 42 (25 requested) atoms. Cycle 9: After refmac, R = 0.1859 (Rfree = 0.000) for 10758 atoms. Found 32 (51 requested) and removed 35 (25 requested) atoms. Cycle 10: After refmac, R = 0.1683 (Rfree = 0.000) for 10726 atoms. Found 14 (51 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 11077 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 11092 seeds are put forward Round 1: 645 peptides, 114 chains. Longest chain 13 peptides. Score 0.361 Round 2: 727 peptides, 105 chains. Longest chain 24 peptides. Score 0.468 Round 3: 753 peptides, 112 chains. Longest chain 20 peptides. Score 0.464 Round 4: 742 peptides, 103 chains. Longest chain 23 peptides. Score 0.488 Round 5: 751 peptides, 104 chains. Longest chain 26 peptides. Score 0.491 Taking the results from Round 5 Chains 104, Residues 647, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26707 restraints for refining 11053 atoms. 24223 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2057 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 45 (26 requested) atoms. Cycle 12: After refmac, R = 0.1897 (Rfree = 0.000) for 10960 atoms. Found 46 (52 requested) and removed 38 (26 requested) atoms. Cycle 13: After refmac, R = 0.1964 (Rfree = 0.000) for 10918 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 14: After refmac, R = 0.1539 (Rfree = 0.000) for 10875 atoms. Found 13 (51 requested) and removed 38 (25 requested) atoms. Cycle 15: After refmac, R = 0.1487 (Rfree = 0.000) for 10823 atoms. Found 19 (51 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.32 Search for helices and strands: 0 residues in 0 chains, 11187 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 11202 seeds are put forward Round 1: 621 peptides, 120 chains. Longest chain 13 peptides. Score 0.314 Round 2: 705 peptides, 111 chains. Longest chain 16 peptides. Score 0.427 Round 3: 721 peptides, 109 chains. Longest chain 16 peptides. Score 0.448 Round 4: 729 peptides, 104 chains. Longest chain 25 peptides. Score 0.473 Round 5: 718 peptides, 105 chains. Longest chain 16 peptides. Score 0.461 Taking the results from Round 4 Chains 104, Residues 625, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26538 restraints for refining 11053 atoms. 24067 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1973 (Rfree = 0.000) for 11053 atoms. Found 49 (52 requested) and removed 32 (26 requested) atoms. Cycle 17: After refmac, R = 0.1901 (Rfree = 0.000) for 10986 atoms. Found 52 (52 requested) and removed 37 (26 requested) atoms. Cycle 18: After refmac, R = 0.1887 (Rfree = 0.000) for 10953 atoms. Found 52 (52 requested) and removed 40 (26 requested) atoms. Cycle 19: After refmac, R = 0.1764 (Rfree = 0.000) for 10921 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 20: After refmac, R = 0.1492 (Rfree = 0.000) for 10899 atoms. Found 16 (51 requested) and removed 27 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.30 Search for helices and strands: 0 residues in 0 chains, 11198 seeds are put forward NCS extension: 43 residues added (5 deleted due to clashes), 11241 seeds are put forward Round 1: 586 peptides, 115 chains. Longest chain 10 peptides. Score 0.301 Round 2: 677 peptides, 114 chains. Longest chain 15 peptides. Score 0.391 Round 3: 699 peptides, 111 chains. Longest chain 17 peptides. Score 0.422 Round 4: 711 peptides, 107 chains. Longest chain 23 peptides. Score 0.447 Round 5: 721 peptides, 112 chains. Longest chain 20 peptides. Score 0.437 Taking the results from Round 4 Chains 108, Residues 604, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26838 restraints for refining 11053 atoms. 24492 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2044 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 46 (26 requested) atoms. Cycle 22: After refmac, R = 0.1999 (Rfree = 0.000) for 10988 atoms. Found 52 (52 requested) and removed 39 (26 requested) atoms. Cycle 23: After refmac, R = 0.2012 (Rfree = 0.000) for 10944 atoms. Found 52 (52 requested) and removed 48 (26 requested) atoms. Cycle 24: After refmac, R = 0.1604 (Rfree = 0.000) for 10895 atoms. Found 23 (51 requested) and removed 38 (25 requested) atoms. Cycle 25: After refmac, R = 0.1537 (Rfree = 0.000) for 10850 atoms. Found 26 (51 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 11163 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 11186 seeds are put forward Round 1: 585 peptides, 117 chains. Longest chain 10 peptides. Score 0.291 Round 2: 662 peptides, 113 chains. Longest chain 12 peptides. Score 0.381 Round 3: 684 peptides, 111 chains. Longest chain 18 peptides. Score 0.409 Round 4: 702 peptides, 108 chains. Longest chain 19 peptides. Score 0.436 Round 5: 722 peptides, 109 chains. Longest chain 23 peptides. Score 0.449 Taking the results from Round 5 Chains 109, Residues 613, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26817 restraints for refining 11051 atoms. 24474 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2059 (Rfree = 0.000) for 11051 atoms. Found 52 (52 requested) and removed 37 (26 requested) atoms. Cycle 27: After refmac, R = 0.1993 (Rfree = 0.000) for 11003 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 28: After refmac, R = 0.1687 (Rfree = 0.000) for 10961 atoms. Found 19 (52 requested) and removed 29 (26 requested) atoms. Cycle 29: After refmac, R = 0.1604 (Rfree = 0.000) for 10909 atoms. Found 17 (51 requested) and removed 37 (25 requested) atoms. Cycle 30: After refmac, R = 0.1583 (Rfree = 0.000) for 10878 atoms. Found 14 (51 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 11210 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 11241 seeds are put forward Round 1: 559 peptides, 109 chains. Longest chain 12 peptides. Score 0.299 Round 2: 651 peptides, 114 chains. Longest chain 14 peptides. Score 0.367 Round 3: 662 peptides, 107 chains. Longest chain 16 peptides. Score 0.405 Round 4: 664 peptides, 109 chains. Longest chain 15 peptides. Score 0.399 Round 5: 660 peptides, 101 chains. Longest chain 18 peptides. Score 0.426 Taking the results from Round 5 Chains 101, Residues 559, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 27420 restraints for refining 11053 atoms. 25285 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2107 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 30 (26 requested) atoms. Cycle 32: After refmac, R = 0.2092 (Rfree = 0.000) for 10966 atoms. Found 52 (52 requested) and removed 43 (26 requested) atoms. Cycle 33: After refmac, R = 0.2032 (Rfree = 0.000) for 10919 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 34: After refmac, R = 0.1918 (Rfree = 0.000) for 10894 atoms. Found 51 (51 requested) and removed 34 (25 requested) atoms. Cycle 35: After refmac, R = 0.1518 (Rfree = 0.000) for 10889 atoms. Found 23 (51 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.32 Search for helices and strands: 0 residues in 0 chains, 11178 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 11197 seeds are put forward Round 1: 512 peptides, 108 chains. Longest chain 10 peptides. Score 0.255 Round 2: 590 peptides, 109 chains. Longest chain 15 peptides. Score 0.330 Round 3: 651 peptides, 116 chains. Longest chain 18 peptides. Score 0.359 Round 4: 647 peptides, 112 chains. Longest chain 14 peptides. Score 0.371 Round 5: 645 peptides, 113 chains. Longest chain 16 peptides. Score 0.366 Taking the results from Round 4 Chains 112, Residues 535, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 27664 restraints for refining 11052 atoms. 25636 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2145 (Rfree = 0.000) for 11052 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 37: After refmac, R = 0.1940 (Rfree = 0.000) for 10998 atoms. Found 52 (52 requested) and removed 43 (26 requested) atoms. Cycle 38: After refmac, R = 0.2006 (Rfree = 0.000) for 10966 atoms. Found 52 (52 requested) and removed 39 (26 requested) atoms. Cycle 39: After refmac, R = 0.1612 (Rfree = 0.000) for 10954 atoms. Found 14 (52 requested) and removed 32 (26 requested) atoms. Cycle 40: After refmac, R = 0.1535 (Rfree = 0.000) for 10917 atoms. Found 17 (51 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 11249 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 11261 seeds are put forward Round 1: 496 peptides, 104 chains. Longest chain 9 peptides. Score 0.256 Round 2: 595 peptides, 103 chains. Longest chain 13 peptides. Score 0.359 Round 3: 624 peptides, 101 chains. Longest chain 18 peptides. Score 0.394 Round 4: 605 peptides, 104 chains. Longest chain 16 peptides. Score 0.365 Round 5: 598 peptides, 99 chains. Longest chain 19 peptides. Score 0.379 Taking the results from Round 3 Chains 101, Residues 523, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 27030 restraints for refining 11053 atoms. 25039 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2075 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 92 (26 requested) atoms. Cycle 42: After refmac, R = 0.1970 (Rfree = 0.000) for 10948 atoms. Found 52 (52 requested) and removed 62 (26 requested) atoms. Cycle 43: After refmac, R = 0.2047 (Rfree = 0.000) for 10896 atoms. Found 51 (51 requested) and removed 61 (25 requested) atoms. Cycle 44: After refmac, R = 0.2005 (Rfree = 0.000) for 10846 atoms. Found 51 (51 requested) and removed 53 (25 requested) atoms. Cycle 45: After refmac, R = 0.1635 (Rfree = 0.000) for 10821 atoms. Found 41 (51 requested) and removed 34 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 11153 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11169 seeds are put forward Round 1: 508 peptides, 110 chains. Longest chain 7 peptides. Score 0.242 Round 2: 574 peptides, 108 chains. Longest chain 12 peptides. Score 0.318 Round 3: 574 peptides, 102 chains. Longest chain 11 peptides. Score 0.344 Round 4: 582 peptides, 97 chains. Longest chain 16 peptides. Score 0.372 Round 5: 609 peptides, 109 chains. Longest chain 14 peptides. Score 0.348 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 97, Residues 485, 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 2anu-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14900 reflections ( 99.71 % complete ) and 27614 restraints for refining 11053 atoms. 25771 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2047 (Rfree = 0.000) for 11053 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.1999 (Rfree = 0.000) for 10968 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.1945 (Rfree = 0.000) for 10917 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.1909 (Rfree = 0.000) for 10857 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:12:43 GMT 2018 Job finished. TimeTaking 130.91 Used memory is bytes: 5433840