Mon 24 Dec 07:55:07 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2anu-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2anu-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-3.8-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 07:55:11 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-3.8-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 1241 and 0 Target number of residues in the AU: 1241 Target solvent content: 0.6322 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-3.8-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-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 12240 target number of atoms Had to go as low as 0.80 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 3.800 Wilson plot Bfac: 67.68 17399 reflections ( 99.75 % complete ) and 0 restraints for refining 13510 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.2989 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2913 (Rfree = 0.000) for 13510 atoms. Found 74 (74 requested) and removed 59 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 13751 seeds are put forward NCS extension: 0 residues added, 13751 seeds are put forward Round 1: 549 peptides, 107 chains. Longest chain 19 peptides. Score 0.298 Round 2: 745 peptides, 117 chains. Longest chain 15 peptides. Score 0.439 Round 3: 778 peptides, 106 chains. Longest chain 32 peptides. Score 0.505 Round 4: 812 peptides, 106 chains. Longest chain 29 peptides. Score 0.531 Round 5: 852 peptides, 111 chains. Longest chain 22 peptides. Score 0.544 Taking the results from Round 5 Chains 111, Residues 741, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26064 restraints for refining 11068 atoms. 23211 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2584 (Rfree = 0.000) for 11068 atoms. Found 60 (60 requested) and removed 64 (30 requested) atoms. Cycle 2: After refmac, R = 0.2402 (Rfree = 0.000) for 10884 atoms. Found 60 (60 requested) and removed 55 (30 requested) atoms. Cycle 3: After refmac, R = 0.2401 (Rfree = 0.000) for 10755 atoms. Found 59 (59 requested) and removed 69 (29 requested) atoms. Cycle 4: After refmac, R = 0.2365 (Rfree = 0.000) for 10670 atoms. Found 59 (59 requested) and removed 52 (29 requested) atoms. Cycle 5: After refmac, R = 0.2301 (Rfree = 0.000) for 10624 atoms. Found 58 (58 requested) and removed 54 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 10941 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 10959 seeds are put forward Round 1: 747 peptides, 123 chains. Longest chain 18 peptides. Score 0.418 Round 2: 826 peptides, 111 chains. Longest chain 20 peptides. Score 0.525 Round 3: 849 peptides, 109 chains. Longest chain 32 peptides. Score 0.549 Round 4: 832 peptides, 103 chains. Longest chain 28 peptides. Score 0.556 Round 5: 842 peptides, 106 chains. Longest chain 24 peptides. Score 0.553 Taking the results from Round 4 Chains 105, Residues 729, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 25825 restraints for refining 11068 atoms. 22924 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2357 (Rfree = 0.000) for 11068 atoms. Found 60 (60 requested) and removed 79 (30 requested) atoms. Cycle 7: After refmac, R = 0.2220 (Rfree = 0.000) for 10945 atoms. Found 60 (60 requested) and removed 70 (30 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2249 (Rfree = 0.000) for 10870 atoms. Found 60 (60 requested) and removed 65 (30 requested) atoms. Cycle 9: After refmac, R = 0.2037 (Rfree = 0.000) for 10818 atoms. Found 59 (59 requested) and removed 50 (29 requested) atoms. Cycle 10: After refmac, R = 0.1778 (Rfree = 0.000) for 10788 atoms. Found 22 (59 requested) and removed 42 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 11154 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 11183 seeds are put forward Round 1: 732 peptides, 120 chains. Longest chain 14 peptides. Score 0.416 Round 2: 800 peptides, 115 chains. Longest chain 17 peptides. Score 0.491 Round 3: 790 peptides, 104 chains. Longest chain 18 peptides. Score 0.522 Round 4: 788 peptides, 106 chains. Longest chain 23 peptides. Score 0.513 Round 5: 787 peptides, 108 chains. Longest chain 18 peptides. Score 0.505 Taking the results from Round 3 Chains 105, Residues 686, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26199 restraints for refining 11070 atoms. 23508 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2288 (Rfree = 0.000) for 11070 atoms. Found 60 (60 requested) and removed 46 (30 requested) atoms. Cycle 12: After refmac, R = 0.2293 (Rfree = 0.000) for 11017 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2212 (Rfree = 0.000) for 10968 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2157 (Rfree = 0.000) for 10939 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 15: After refmac, R = 0.2101 (Rfree = 0.000) for 10917 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.23 Search for helices and strands: 0 residues in 0 chains, 11253 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 11280 seeds are put forward Round 1: 724 peptides, 130 chains. Longest chain 20 peptides. Score 0.371 Round 2: 788 peptides, 124 chains. Longest chain 22 peptides. Score 0.449 Round 3: 787 peptides, 119 chains. Longest chain 19 peptides. Score 0.466 Round 4: 813 peptides, 116 chains. Longest chain 19 peptides. Score 0.498 Round 5: 797 peptides, 109 chains. Longest chain 23 peptides. Score 0.510 Taking the results from Round 5 Chains 109, Residues 688, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26651 restraints for refining 11070 atoms. 24008 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2243 (Rfree = 0.000) for 11070 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. Cycle 17: After refmac, R = 0.2114 (Rfree = 0.000) for 10979 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 18: After refmac, R = 0.2058 (Rfree = 0.000) for 10918 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 19: After refmac, R = 0.2037 (Rfree = 0.000) for 10899 atoms. Found 60 (60 requested) and removed 42 (30 requested) atoms. Cycle 20: After refmac, R = 0.1726 (Rfree = 0.000) for 10885 atoms. Found 24 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 11194 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 11219 seeds are put forward Round 1: 689 peptides, 122 chains. Longest chain 14 peptides. Score 0.370 Round 2: 760 peptides, 119 chains. Longest chain 19 peptides. Score 0.444 Round 3: 787 peptides, 122 chains. Longest chain 19 peptides. Score 0.456 Round 4: 821 peptides, 118 chains. Longest chain 21 peptides. Score 0.497 Round 5: 806 peptides, 121 chains. Longest chain 19 peptides. Score 0.475 Taking the results from Round 4 Chains 118, Residues 703, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26479 restraints for refining 11069 atoms. 23785 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2231 (Rfree = 0.000) for 11069 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. Cycle 22: After refmac, R = 0.2202 (Rfree = 0.000) for 10979 atoms. Found 60 (60 requested) and removed 63 (30 requested) atoms. Cycle 23: After refmac, R = 0.2113 (Rfree = 0.000) for 10926 atoms. Found 60 (60 requested) and removed 54 (30 requested) atoms. Cycle 24: After refmac, R = 0.2106 (Rfree = 0.000) for 10888 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. Cycle 25: After refmac, R = 0.1838 (Rfree = 0.000) for 10864 atoms. Found 19 (59 requested) and removed 39 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 11180 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 11204 seeds are put forward Round 1: 649 peptides, 115 chains. Longest chain 14 peptides. Score 0.361 Round 2: 738 peptides, 107 chains. Longest chain 21 peptides. Score 0.470 Round 3: 786 peptides, 113 chains. Longest chain 26 peptides. Score 0.487 Round 4: 770 peptides, 110 chains. Longest chain 19 peptides. Score 0.485 Round 5: 746 peptides, 98 chains. Longest chain 25 peptides. Score 0.509 Taking the results from Round 5 Chains 100, Residues 648, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26459 restraints for refining 11070 atoms. 23816 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2309 (Rfree = 0.000) for 11070 atoms. Found 60 (60 requested) and removed 52 (30 requested) atoms. Cycle 27: After refmac, R = 0.2243 (Rfree = 0.000) for 10995 atoms. Found 60 (60 requested) and removed 37 (30 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2223 (Rfree = 0.000) for 10965 atoms. Found 60 (60 requested) and removed 42 (30 requested) atoms. Cycle 29: After refmac, R = 0.1873 (Rfree = 0.000) for 10937 atoms. Found 35 (60 requested) and removed 37 (30 requested) atoms. Cycle 30: After refmac, R = 0.1786 (Rfree = 0.000) for 10905 atoms. Found 25 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.27 Search for helices and strands: 0 residues in 0 chains, 11255 seeds are put forward NCS extension: 34 residues added (4 deleted due to clashes), 11289 seeds are put forward Round 1: 645 peptides, 121 chains. Longest chain 11 peptides. Score 0.333 Round 2: 741 peptides, 117 chains. Longest chain 16 peptides. Score 0.435 Round 3: 746 peptides, 114 chains. Longest chain 14 peptides. Score 0.451 Round 4: 763 peptides, 111 chains. Longest chain 20 peptides. Score 0.476 Round 5: 780 peptides, 121 chains. Longest chain 18 peptides. Score 0.453 Taking the results from Round 4 Chains 111, Residues 652, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26708 restraints for refining 11070 atoms. 24211 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2231 (Rfree = 0.000) for 11070 atoms. Found 60 (60 requested) and removed 46 (30 requested) atoms. Cycle 32: After refmac, R = 0.2205 (Rfree = 0.000) for 11021 atoms. Found 60 (60 requested) and removed 52 (30 requested) atoms. Cycle 33: After refmac, R = 0.2114 (Rfree = 0.000) for 10979 atoms. Found 60 (60 requested) and removed 50 (30 requested) atoms. Cycle 34: After refmac, R = 0.2096 (Rfree = 0.000) for 10957 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 35: After refmac, R = 0.2038 (Rfree = 0.000) for 10955 atoms. Found 60 (60 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 11320 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 11348 seeds are put forward Round 1: 608 peptides, 122 chains. Longest chain 12 peptides. Score 0.293 Round 2: 663 peptides, 113 chains. Longest chain 18 peptides. Score 0.382 Round 3: 716 peptides, 117 chains. Longest chain 16 peptides. Score 0.414 Round 4: 693 peptides, 113 chains. Longest chain 21 peptides. Score 0.409 Round 5: 717 peptides, 116 chains. Longest chain 15 peptides. Score 0.418 Taking the results from Round 5 Chains 116, Residues 601, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26642 restraints for refining 11071 atoms. 24354 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2195 (Rfree = 0.000) for 11071 atoms. Found 60 (60 requested) and removed 44 (30 requested) atoms. Cycle 37: After refmac, R = 0.2132 (Rfree = 0.000) for 11003 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 38: After refmac, R = 0.2219 (Rfree = 0.000) for 10964 atoms. Found 60 (60 requested) and removed 43 (30 requested) atoms. Cycle 39: After refmac, R = 0.2097 (Rfree = 0.000) for 10939 atoms. Found 60 (60 requested) and removed 43 (30 requested) atoms. Cycle 40: After refmac, R = 0.1771 (Rfree = 0.000) for 10924 atoms. Found 38 (60 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 11292 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 11306 seeds are put forward Round 1: 571 peptides, 121 chains. Longest chain 15 peptides. Score 0.260 Round 2: 681 peptides, 120 chains. Longest chain 16 peptides. Score 0.371 Round 3: 664 peptides, 106 chains. Longest chain 19 peptides. Score 0.411 Round 4: 655 peptides, 110 chains. Longest chain 13 peptides. Score 0.387 Round 5: 702 peptides, 108 chains. Longest chain 21 peptides. Score 0.436 Taking the results from Round 5 Chains 108, Residues 594, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26800 restraints for refining 11068 atoms. 24532 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2207 (Rfree = 0.000) for 11068 atoms. Found 60 (60 requested) and removed 59 (30 requested) atoms. Cycle 42: After refmac, R = 0.2128 (Rfree = 0.000) for 11001 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 43: After refmac, R = 0.2078 (Rfree = 0.000) for 10949 atoms. Found 60 (60 requested) and removed 46 (30 requested) atoms. Cycle 44: After refmac, R = 0.1779 (Rfree = 0.000) for 10934 atoms. Found 47 (60 requested) and removed 38 (30 requested) atoms. Cycle 45: After refmac, R = 0.1711 (Rfree = 0.000) for 10917 atoms. Found 20 (60 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 11201 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 11237 seeds are put forward Round 1: 507 peptides, 107 chains. Longest chain 11 peptides. Score 0.255 Round 2: 591 peptides, 102 chains. Longest chain 18 peptides. Score 0.360 Round 3: 593 peptides, 102 chains. Longest chain 14 peptides. Score 0.362 Round 4: 595 peptides, 98 chains. Longest chain 15 peptides. Score 0.380 Round 5: 601 peptides, 96 chains. Longest chain 17 peptides. Score 0.394 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 96, Residues 505, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17399 reflections ( 99.75 % complete ) and 27405 restraints for refining 11071 atoms. 25481 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2249 (Rfree = 0.000) for 11071 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 47: After refmac, R = 0.2234 (Rfree = 0.000) for 11002 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 48: After refmac, R = 0.2207 (Rfree = 0.000) for 10941 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 49: After refmac, R = 0.2292 (Rfree = 0.000) for 10894 atoms. TimeTaking 132.17