Mon 24 Dec 00:18:13 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 2awa-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-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/2awa-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-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 00:18:18 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/2awa-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-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 1114 and 0 Target number of residues in the AU: 1114 Target solvent content: 0.6673 Checking the provided sequence file Detected sequence length: 390 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1560 Adjusted target solvent content: 0.53 Input MTZ file: 2awa-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: 4 Cell parameters: 94.281 70.854 135.686 90.000 91.232 90.000 Input sequence file: 2awa-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12480 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: 135.654 4.000 Wilson plot Bfac: 90.32 14641 reflections ( 94.66 % complete ) and 0 restraints for refining 13748 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3510 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3331 (Rfree = 0.000) for 13748 atoms. Found 65 (65 requested) and removed 97 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.68 Search for helices and strands: 0 residues in 0 chains, 13881 seeds are put forward NCS extension: 0 residues added, 13881 seeds are put forward Round 1: 379 peptides, 81 chains. Longest chain 9 peptides. Score 0.234 Round 2: 496 peptides, 97 chains. Longest chain 15 peptides. Score 0.288 Round 3: 543 peptides, 106 chains. Longest chain 13 peptides. Score 0.297 Round 4: 591 peptides, 104 chains. Longest chain 13 peptides. Score 0.353 Round 5: 613 peptides, 105 chains. Longest chain 17 peptides. Score 0.369 Taking the results from Round 5 Chains 105, Residues 508, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 27661 restraints for refining 11268 atoms. 25704 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2603 (Rfree = 0.000) for 11268 atoms. Found 26 (53 requested) and removed 77 (26 requested) atoms. Cycle 2: After refmac, R = 0.2354 (Rfree = 0.000) for 11038 atoms. Found 39 (53 requested) and removed 70 (26 requested) atoms. Cycle 3: After refmac, R = 0.2248 (Rfree = 0.000) for 10910 atoms. Found 42 (52 requested) and removed 68 (26 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2153 (Rfree = 0.000) for 10809 atoms. Found 36 (51 requested) and removed 73 (25 requested) atoms. Cycle 5: After refmac, R = 0.2069 (Rfree = 0.000) for 10727 atoms. Found 33 (51 requested) and removed 65 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 10959 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10973 seeds are put forward Round 1: 577 peptides, 118 chains. Longest chain 9 peptides. Score 0.280 Round 2: 637 peptides, 110 chains. Longest chain 13 peptides. Score 0.371 Round 3: 661 peptides, 110 chains. Longest chain 14 peptides. Score 0.393 Round 4: 685 peptides, 113 chains. Longest chain 22 peptides. Score 0.403 Round 5: 684 peptides, 110 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 5 Chains 110, Residues 574, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26104 restraints for refining 11086 atoms. 23918 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2016 (Rfree = 0.000) for 11086 atoms. Found 36 (52 requested) and removed 97 (26 requested) atoms. Cycle 7: After refmac, R = 0.2063 (Rfree = 0.000) for 10944 atoms. Found 49 (52 requested) and removed 85 (26 requested) atoms. Cycle 8: After refmac, R = 0.1944 (Rfree = 0.000) for 10867 atoms. Found 51 (51 requested) and removed 64 (25 requested) atoms. Cycle 9: After refmac, R = 0.1854 (Rfree = 0.000) for 10817 atoms. Found 45 (51 requested) and removed 61 (25 requested) atoms. Cycle 10: After refmac, R = 0.1894 (Rfree = 0.000) for 10769 atoms. Found 51 (51 requested) and removed 44 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 11087 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 11101 seeds are put forward Round 1: 610 peptides, 126 chains. Longest chain 11 peptides. Score 0.279 Round 2: 677 peptides, 119 chains. Longest chain 15 peptides. Score 0.372 Round 3: 690 peptides, 116 chains. Longest chain 16 peptides. Score 0.396 Round 4: 683 peptides, 111 chains. Longest chain 13 peptides. Score 0.409 Round 5: 714 peptides, 115 chains. Longest chain 17 peptides. Score 0.421 Taking the results from Round 5 Chains 116, Residues 599, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26083 restraints for refining 11269 atoms. 23738 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1997 (Rfree = 0.000) for 11269 atoms. Found 20 (53 requested) and removed 66 (26 requested) atoms. Cycle 12: After refmac, R = 0.1980 (Rfree = 0.000) for 11142 atoms. Found 46 (53 requested) and removed 60 (26 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1876 (Rfree = 0.000) for 11084 atoms. Found 40 (52 requested) and removed 54 (26 requested) atoms. Cycle 14: After refmac, R = 0.1816 (Rfree = 0.000) for 11030 atoms. Found 49 (52 requested) and removed 51 (26 requested) atoms. Cycle 15: After refmac, R = 0.1819 (Rfree = 0.000) for 11005 atoms. Found 52 (52 requested) and removed 54 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.61 Search for helices and strands: 0 residues in 0 chains, 11289 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 11303 seeds are put forward Round 1: 571 peptides, 118 chains. Longest chain 11 peptides. Score 0.274 Round 2: 663 peptides, 115 chains. Longest chain 14 peptides. Score 0.375 Round 3: 678 peptides, 109 chains. Longest chain 22 peptides. Score 0.412 Round 4: 652 peptides, 106 chains. Longest chain 17 peptides. Score 0.401 Round 5: 651 peptides, 107 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 3 Chains 109, Residues 569, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14641 reflections ( 94.66 % complete ) and 26061 restraints for refining 11267 atoms. 23872 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1876 (Rfree = 0.000) for 11267 atoms. Found 36 (53 requested) and removed 55 (26 requested) atoms. Cycle 17: After refmac, R = 0.1813 (Rfree = 0.000) for 11184 atoms. Found 48 (53 requested) and removed 53 (26 requested) atoms. Cycle 18: After refmac, R = 0.1664 (Rfree = 0.000) for 11145 atoms. Found 36 (53 requested) and removed 56 (26 requested) atoms. Cycle 19: After refmac, R = 0.1697 (Rfree = 0.000) for 11103 atoms. Found 40 (52 requested) and removed 49 (26 requested) atoms. Cycle 20: After refmac, R = 0.1639 (Rfree = 0.000) for 11076 atoms. Found 45 (52 requested) and removed 43 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 11396 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 11433 seeds are put forward Round 1: 575 peptides, 119 chains. Longest chain 9 peptides. Score 0.273 Round 2: 686 peptides, 126 chains. Longest chain 13 peptides. Score 0.353 Round 3: 698 peptides, 124 chains. Longest chain 12 peptides. Score 0.372 Round 4: 688 peptides, 115 chains. Longest chain 14 peptides. Score 0.398 Round 5: 672 peptides, 115 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 4 Chains 115, Residues 573, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26156 restraints for refining 11269 atoms. 23937 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1903 (Rfree = 0.000) for 11269 atoms. Found 36 (53 requested) and removed 56 (26 requested) atoms. Cycle 22: After refmac, R = 0.1777 (Rfree = 0.000) for 11192 atoms. Found 43 (53 requested) and removed 58 (26 requested) atoms. Cycle 23: After refmac, R = 0.1715 (Rfree = 0.000) for 11154 atoms. Found 39 (53 requested) and removed 48 (26 requested) atoms. Cycle 24: After refmac, R = 0.1651 (Rfree = 0.000) for 11126 atoms. Found 42 (52 requested) and removed 37 (26 requested) atoms. Cycle 25: After refmac, R = 0.1286 (Rfree = 0.000) for 11114 atoms. Found 4 (52 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 11315 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 11333 seeds are put forward Round 1: 592 peptides, 125 chains. Longest chain 10 peptides. Score 0.265 Round 2: 627 peptides, 113 chains. Longest chain 12 peptides. Score 0.350 Round 3: 649 peptides, 112 chains. Longest chain 12 peptides. Score 0.374 Round 4: 624 peptides, 109 chains. Longest chain 15 peptides. Score 0.363 Round 5: 653 peptides, 112 chains. Longest chain 16 peptides. Score 0.378 Taking the results from Round 5 Chains 112, Residues 541, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14641 reflections ( 94.66 % complete ) and 26476 restraints for refining 11268 atoms. 24424 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1940 (Rfree = 0.000) for 11268 atoms. Found 35 (53 requested) and removed 47 (26 requested) atoms. Cycle 27: After refmac, R = 0.1889 (Rfree = 0.000) for 11181 atoms. Found 53 (53 requested) and removed 41 (26 requested) atoms. Cycle 28: After refmac, R = 0.1841 (Rfree = 0.000) for 11141 atoms. Found 52 (53 requested) and removed 40 (26 requested) atoms. Cycle 29: After refmac, R = 0.1834 (Rfree = 0.000) for 11097 atoms. Found 52 (52 requested) and removed 40 (26 requested) atoms. Cycle 30: After refmac, R = 0.1845 (Rfree = 0.000) for 11078 atoms. Found 52 (52 requested) and removed 45 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 11342 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 11364 seeds are put forward Round 1: 496 peptides, 106 chains. Longest chain 11 peptides. Score 0.248 Round 2: 574 peptides, 108 chains. Longest chain 11 peptides. Score 0.319 Round 3: 566 peptides, 98 chains. Longest chain 11 peptides. Score 0.354 Round 4: 603 peptides, 106 chains. Longest chain 10 peptides. Score 0.356 Round 5: 604 peptides, 105 chains. Longest chain 15 peptides. Score 0.361 Taking the results from Round 5 Chains 105, Residues 499, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26759 restraints for refining 11268 atoms. 24868 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2027 (Rfree = 0.000) for 11268 atoms. Found 53 (53 requested) and removed 48 (26 requested) atoms. Cycle 32: After refmac, R = 0.1838 (Rfree = 0.000) for 11186 atoms. Found 53 (53 requested) and removed 38 (26 requested) atoms. Cycle 33: After refmac, R = 0.1456 (Rfree = 0.000) for 11162 atoms. Found 11 (53 requested) and removed 31 (26 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1315 (Rfree = 0.000) for 11118 atoms. Found 8 (52 requested) and removed 28 (26 requested) atoms. Cycle 35: After refmac, R = 0.1279 (Rfree = 0.000) for 11087 atoms. Found 10 (52 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 11271 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 11294 seeds are put forward Round 1: 456 peptides, 99 chains. Longest chain 10 peptides. Score 0.236 Round 2: 561 peptides, 111 chains. Longest chain 11 peptides. Score 0.293 Round 3: 573 peptides, 108 chains. Longest chain 13 peptides. Score 0.318 Round 4: 584 peptides, 104 chains. Longest chain 13 peptides. Score 0.346 Round 5: 599 peptides, 104 chains. Longest chain 17 peptides. Score 0.360 Taking the results from Round 5 Chains 104, Residues 495, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26686 restraints for refining 11270 atoms. 24810 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1912 (Rfree = 0.000) for 11270 atoms. Found 42 (53 requested) and removed 41 (26 requested) atoms. Cycle 37: After refmac, R = 0.1857 (Rfree = 0.000) for 11198 atoms. Found 53 (53 requested) and removed 37 (26 requested) atoms. Cycle 38: After refmac, R = 0.1877 (Rfree = 0.000) for 11166 atoms. Found 53 (53 requested) and removed 44 (26 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1758 (Rfree = 0.000) for 11133 atoms. Found 53 (53 requested) and removed 39 (26 requested) atoms. Cycle 40: After refmac, R = 0.1796 (Rfree = 0.000) for 11119 atoms. Found 52 (52 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 11327 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 11346 seeds are put forward Round 1: 428 peptides, 95 chains. Longest chain 8 peptides. Score 0.223 Round 2: 494 peptides, 100 chains. Longest chain 9 peptides. Score 0.272 Round 3: 509 peptides, 97 chains. Longest chain 12 peptides. Score 0.301 Round 4: 496 peptides, 90 chains. Longest chain 13 peptides. Score 0.319 Round 5: 514 peptides, 93 chains. Longest chain 12 peptides. Score 0.324 Taking the results from Round 5 Chains 93, Residues 421, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 27001 restraints for refining 11268 atoms. 25410 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1976 (Rfree = 0.000) for 11268 atoms. Found 50 (53 requested) and removed 43 (26 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1880 (Rfree = 0.000) for 11215 atoms. Found 53 (53 requested) and removed 48 (26 requested) atoms. Cycle 43: After refmac, R = 0.1859 (Rfree = 0.000) for 11179 atoms. Found 53 (53 requested) and removed 42 (26 requested) atoms. Cycle 44: After refmac, R = 0.1911 (Rfree = 0.000) for 11157 atoms. Found 53 (53 requested) and removed 42 (26 requested) atoms. Cycle 45: After refmac, R = 0.1857 (Rfree = 0.000) for 11133 atoms. Found 53 (53 requested) and removed 37 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 11334 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11354 seeds are put forward Round 1: 387 peptides, 88 chains. Longest chain 8 peptides. Score 0.209 Round 2: 438 peptides, 83 chains. Longest chain 13 peptides. Score 0.290 Round 3: 461 peptides, 89 chains. Longest chain 13 peptides. Score 0.287 Round 4: 459 peptides, 82 chains. Longest chain 14 peptides. Score 0.317 Round 5: 465 peptides, 87 chains. Longest chain 15 peptides. Score 0.301 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 82, Residues 377, 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 2awa-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14641 reflections ( 94.66 % complete ) and 26610 restraints for refining 11178 atoms. 25184 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2126 (Rfree = 0.000) for 11178 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.1950 (Rfree = 0.000) for 11096 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1828 (Rfree = 0.000) for 11038 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.1942 (Rfree = 0.000) for 10980 atoms. TimeTaking 104.17