Mon 24 Dec 00:05:04 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ash-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-4.0-parrot-mrncs ############### 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 00:05:09 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-4.0-parrot-mrncs/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-mrncs.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-mrncs.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 13564 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3347 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3333 (Rfree = 0.000) for 13564 atoms. Found 64 (64 requested) and removed 95 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.69 Search for helices and strands: 0 residues in 0 chains, 13770 seeds are put forward NCS extension: 0 residues added, 13770 seeds are put forward Round 1: 508 peptides, 106 chains. Longest chain 11 peptides. Score 0.263 Round 2: 679 peptides, 107 chains. Longest chain 18 peptides. Score 0.427 Round 3: 715 peptides, 114 chains. Longest chain 15 peptides. Score 0.431 Round 4: 731 peptides, 103 chains. Longest chain 18 peptides. Score 0.487 Round 5: 746 peptides, 108 chains. Longest chain 17 peptides. Score 0.481 Taking the results from Round 4 Chains 108, Residues 628, Estimated correctness of the model 0.0 % 8 chains (65 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 25782 restraints for refining 11001 atoms. 23136 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2626 (Rfree = 0.000) for 11001 atoms. Found 52 (52 requested) and removed 76 (26 requested) atoms. Cycle 2: After refmac, R = 0.2369 (Rfree = 0.000) for 10790 atoms. Found 51 (52 requested) and removed 61 (26 requested) atoms. Cycle 3: After refmac, R = 0.2353 (Rfree = 0.000) for 10668 atoms. Found 51 (51 requested) and removed 76 (25 requested) atoms. Cycle 4: After refmac, R = 0.2207 (Rfree = 0.000) for 10584 atoms. Found 50 (50 requested) and removed 62 (25 requested) atoms. Cycle 5: After refmac, R = 0.2225 (Rfree = 0.000) for 10525 atoms. Found 50 (50 requested) and removed 56 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.91 3.76 Search for helices and strands: 0 residues in 0 chains, 10850 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 10867 seeds are put forward Round 1: 640 peptides, 117 chains. Longest chain 12 peptides. Score 0.350 Round 2: 722 peptides, 111 chains. Longest chain 20 peptides. Score 0.449 Round 3: 754 peptides, 99 chains. Longest chain 22 peptides. Score 0.520 Round 4: 751 peptides, 99 chains. Longest chain 25 peptides. Score 0.518 Round 5: 760 peptides, 100 chains. Longest chain 25 peptides. Score 0.522 Taking the results from Round 5 Chains 104, Residues 660, Estimated correctness of the model 0.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14751 reflections ( 99.68 % complete ) and 25525 restraints for refining 11007 atoms. 22856 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2194 (Rfree = 0.000) for 11007 atoms. Found 48 (52 requested) and removed 89 (26 requested) atoms. Cycle 7: After refmac, R = 0.2143 (Rfree = 0.000) for 10849 atoms. Found 52 (52 requested) and removed 51 (26 requested) atoms. Cycle 8: After refmac, R = 0.2069 (Rfree = 0.000) for 10790 atoms. Found 51 (51 requested) and removed 64 (25 requested) atoms. Cycle 9: After refmac, R = 0.1910 (Rfree = 0.000) for 10737 atoms. Found 51 (51 requested) and removed 49 (25 requested) atoms. Cycle 10: After refmac, R = 0.1931 (Rfree = 0.000) for 10707 atoms. Found 51 (51 requested) and removed 58 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.68 Search for helices and strands: 0 residues in 0 chains, 11061 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 11078 seeds are put forward Round 1: 630 peptides, 114 chains. Longest chain 19 peptides. Score 0.353 Round 2: 700 peptides, 106 chains. Longest chain 26 peptides. Score 0.449 Round 3: 735 peptides, 113 chains. Longest chain 15 peptides. Score 0.453 Round 4: 724 peptides, 106 chains. Longest chain 22 peptides. Score 0.470 Round 5: 726 peptides, 101 chains. Longest chain 18 peptides. Score 0.490 Taking the results from Round 5 Chains 104, Residues 625, Estimated correctness of the model 0.0 % 6 chains (51 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 25427 restraints for refining 11009 atoms. 22842 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2164 (Rfree = 0.000) for 11009 atoms. Found 52 (52 requested) and removed 63 (26 requested) atoms. Cycle 12: After refmac, R = 0.1943 (Rfree = 0.000) for 10912 atoms. Found 52 (52 requested) and removed 51 (26 requested) atoms. Cycle 13: After refmac, R = 0.1829 (Rfree = 0.000) for 10853 atoms. Found 46 (51 requested) and removed 53 (25 requested) atoms. Cycle 14: After refmac, R = 0.1409 (Rfree = 0.000) for 10825 atoms. Found 12 (51 requested) and removed 38 (25 requested) atoms. Cycle 15: After refmac, R = 0.1335 (Rfree = 0.000) for 10781 atoms. Found 8 (51 requested) and removed 36 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.85 3.70 Search for helices and strands: 0 residues in 0 chains, 11126 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 11147 seeds are put forward Round 1: 644 peptides, 122 chains. Longest chain 12 peptides. Score 0.333 Round 2: 730 peptides, 119 chains. Longest chain 19 peptides. Score 0.425 Round 3: 733 peptides, 114 chains. Longest chain 17 peptides. Score 0.447 Round 4: 738 peptides, 110 chains. Longest chain 21 peptides. Score 0.467 Round 5: 710 peptides, 104 chains. Longest chain 21 peptides. Score 0.466 Taking the results from Round 4 Chains 111, Residues 628, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 25811 restraints for refining 11010 atoms. 23307 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2094 (Rfree = 0.000) for 11010 atoms. Found 41 (52 requested) and removed 50 (26 requested) atoms. Cycle 17: After refmac, R = 0.1892 (Rfree = 0.000) for 10937 atoms. Found 51 (52 requested) and removed 53 (26 requested) atoms. Cycle 18: After refmac, R = 0.1873 (Rfree = 0.000) for 10892 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. Cycle 19: After refmac, R = 0.1798 (Rfree = 0.000) for 10870 atoms. Found 51 (51 requested) and removed 51 (25 requested) atoms. Cycle 20: After refmac, R = 0.1720 (Rfree = 0.000) for 10846 atoms. Found 44 (51 requested) and removed 39 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 11192 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 11220 seeds are put forward Round 1: 592 peptides, 108 chains. Longest chain 12 peptides. Score 0.341 Round 2: 681 peptides, 111 chains. Longest chain 16 peptides. Score 0.413 Round 3: 715 peptides, 114 chains. Longest chain 22 peptides. Score 0.431 Round 4: 736 peptides, 113 chains. Longest chain 19 peptides. Score 0.454 Round 5: 734 peptides, 110 chains. Longest chain 26 peptides. Score 0.463 Taking the results from Round 5 Chains 112, Residues 624, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 25979 restraints for refining 11009 atoms. 23509 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2058 (Rfree = 0.000) for 11009 atoms. Found 41 (52 requested) and removed 51 (26 requested) atoms. Cycle 22: After refmac, R = 0.1996 (Rfree = 0.000) for 10911 atoms. Found 52 (52 requested) and removed 47 (26 requested) atoms. Cycle 23: After refmac, R = 0.1855 (Rfree = 0.000) for 10886 atoms. Found 40 (51 requested) and removed 45 (25 requested) atoms. Cycle 24: After refmac, R = 0.1753 (Rfree = 0.000) for 10856 atoms. Found 38 (51 requested) and removed 42 (25 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1781 (Rfree = 0.000) for 10831 atoms. Found 51 (51 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 11234 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11254 seeds are put forward Round 1: 609 peptides, 121 chains. Longest chain 12 peptides. Score 0.302 Round 2: 673 peptides, 113 chains. Longest chain 17 peptides. Score 0.397 Round 3: 691 peptides, 115 chains. Longest chain 17 peptides. Score 0.406 Round 4: 705 peptides, 109 chains. Longest chain 23 peptides. Score 0.442 Round 5: 684 peptides, 109 chains. Longest chain 17 peptides. Score 0.423 Taking the results from Round 4 Chains 110, Residues 596, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 26075 restraints for refining 11007 atoms. 23725 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2083 (Rfree = 0.000) for 11007 atoms. Found 52 (52 requested) and removed 46 (26 requested) atoms. Cycle 27: After refmac, R = 0.2097 (Rfree = 0.000) for 10941 atoms. Found 52 (52 requested) and removed 39 (26 requested) atoms. Cycle 28: After refmac, R = 0.1867 (Rfree = 0.000) for 10899 atoms. Found 52 (52 requested) and removed 34 (26 requested) atoms. Cycle 29: After refmac, R = 0.1941 (Rfree = 0.000) for 10863 atoms. Found 51 (51 requested) and removed 39 (25 requested) atoms. Cycle 30: After refmac, R = 0.1442 (Rfree = 0.000) for 10832 atoms. Found 16 (51 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.88 3.73 Search for helices and strands: 0 residues in 0 chains, 11121 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 11159 seeds are put forward Round 1: 548 peptides, 112 chains. Longest chain 13 peptides. Score 0.278 Round 2: 588 peptides, 105 chains. Longest chain 13 peptides. Score 0.349 Round 3: 634 peptides, 108 chains. Longest chain 14 peptides. Score 0.381 Round 4: 671 peptides, 110 chains. Longest chain 22 peptides. Score 0.408 Round 5: 667 peptides, 104 chains. Longest chain 24 peptides. Score 0.428 Taking the results from Round 5 Chains 104, Residues 563, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 26429 restraints for refining 11008 atoms. 24261 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2193 (Rfree = 0.000) for 11008 atoms. Found 52 (52 requested) and removed 47 (26 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1989 (Rfree = 0.000) for 10923 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 33: After refmac, R = 0.1958 (Rfree = 0.000) for 10886 atoms. Found 51 (51 requested) and removed 34 (25 requested) atoms. Cycle 34: After refmac, R = 0.1981 (Rfree = 0.000) for 10862 atoms. Found 51 (51 requested) and removed 45 (25 requested) atoms. Cycle 35: After refmac, R = 0.1913 (Rfree = 0.000) for 10832 atoms. Found 51 (51 requested) and removed 41 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.90 3.75 Search for helices and strands: 0 residues in 0 chains, 11159 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 11182 seeds are put forward Round 1: 455 peptides, 95 chains. Longest chain 12 peptides. Score 0.255 Round 2: 530 peptides, 96 chains. Longest chain 11 peptides. Score 0.330 Round 3: 513 peptides, 87 chains. Longest chain 14 peptides. Score 0.353 Round 4: 515 peptides, 85 chains. Longest chain 14 peptides. Score 0.364 Round 5: 530 peptides, 91 chains. Longest chain 15 peptides. Score 0.352 Taking the results from Round 4 Chains 85, Residues 430, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 27091 restraints for refining 10966 atoms. 25456 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2194 (Rfree = 0.000) for 10966 atoms. Found 52 (52 requested) and removed 47 (26 requested) atoms. Cycle 37: After refmac, R = 0.2153 (Rfree = 0.000) for 10926 atoms. Found 52 (52 requested) and removed 56 (26 requested) atoms. Cycle 38: After refmac, R = 0.1948 (Rfree = 0.000) for 10883 atoms. Found 51 (51 requested) and removed 42 (25 requested) atoms. Cycle 39: After refmac, R = 0.2040 (Rfree = 0.000) for 10858 atoms. Found 51 (51 requested) and removed 44 (25 requested) atoms. Cycle 40: After refmac, R = 0.2019 (Rfree = 0.000) for 10835 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.84 3.69 Search for helices and strands: 0 residues in 0 chains, 11208 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 11223 seeds are put forward Round 1: 410 peptides, 89 chains. Longest chain 7 peptides. Score 0.233 Round 2: 495 peptides, 96 chains. Longest chain 9 peptides. Score 0.294 Round 3: 505 peptides, 94 chains. Longest chain 10 peptides. Score 0.314 Round 4: 555 peptides, 98 chains. Longest chain 11 peptides. Score 0.347 Round 5: 544 peptides, 92 chains. Longest chain 15 peptides. Score 0.362 Taking the results from Round 5 Chains 92, Residues 452, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 14751 reflections ( 99.68 % complete ) and 26228 restraints for refining 10949 atoms. 24469 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2138 (Rfree = 0.000) for 10949 atoms. Found 52 (52 requested) and removed 62 (26 requested) atoms. Cycle 42: After refmac, R = 0.2064 (Rfree = 0.000) for 10857 atoms. Found 51 (51 requested) and removed 47 (25 requested) atoms. Cycle 43: After refmac, R = 0.1990 (Rfree = 0.000) for 10813 atoms. Found 51 (51 requested) and removed 54 (25 requested) atoms. Cycle 44: After refmac, R = 0.1537 (Rfree = 0.000) for 10768 atoms. Found 30 (51 requested) and removed 34 (25 requested) atoms. Cycle 45: After refmac, R = 0.1366 (Rfree = 0.000) for 10751 atoms. Found 16 (51 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.88 3.73 Search for helices and strands: 0 residues in 0 chains, 11090 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 11109 seeds are put forward Round 1: 470 peptides, 103 chains. Longest chain 9 peptides. Score 0.234 Round 2: 555 peptides, 107 chains. Longest chain 11 peptides. Score 0.308 Round 3: 539 peptides, 97 chains. Longest chain 15 peptides. Score 0.335 Round 4: 539 peptides, 96 chains. Longest chain 21 peptides. Score 0.340 Round 5: 558 peptides, 98 chains. Longest chain 16 peptides. Score 0.350 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 98, Residues 460, 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 2ash-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 14751 reflections ( 99.68 % complete ) and 26206 restraints for refining 10876 atoms. 24464 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2261 (Rfree = 0.000) for 10876 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 47: After refmac, R = 0.2033 (Rfree = 0.000) for 10805 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 48: After refmac, R = 0.2004 (Rfree = 0.000) for 10734 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.2046 (Rfree = 0.000) for 10684 atoms. TimeTaking 113.98