Mon 24 Dec 00:26:53 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 1vl6-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-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/1vl6-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-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 00:26:58 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/1vl6-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-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 1263 and 0 Target number of residues in the AU: 1263 Target solvent content: 0.6504 Checking the provided sequence file Detected sequence length: 388 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1552 Adjusted target solvent content: 0.57 Input MTZ file: 1vl6-3.6-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.90 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: 124.815 3.600 Wilson plot Bfac: 78.40 22267 reflections ( 99.87 % complete ) and 0 restraints for refining 13692 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3377 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3292 (Rfree = 0.000) for 13692 atoms. Found 87 (87 requested) and removed 93 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.27 Search for helices and strands: 0 residues in 0 chains, 13936 seeds are put forward NCS extension: 0 residues added, 13936 seeds are put forward Round 1: 602 peptides, 112 chains. Longest chain 16 peptides. Score 0.321 Round 2: 771 peptides, 114 chains. Longest chain 21 peptides. Score 0.457 Round 3: 834 peptides, 112 chains. Longest chain 22 peptides. Score 0.511 Round 4: 843 peptides, 109 chains. Longest chain 26 peptides. Score 0.527 Round 5: 844 peptides, 107 chains. Longest chain 26 peptides. Score 0.534 Taking the results from Round 5 Chains 112, Residues 737, Estimated correctness of the model 0.0 % 16 chains (152 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 24377 restraints for refining 11247 atoms. 21061 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2921 (Rfree = 0.000) for 11247 atoms. Found 72 (72 requested) and removed 107 (36 requested) atoms. Cycle 2: After refmac, R = 0.2762 (Rfree = 0.000) for 11009 atoms. Found 71 (71 requested) and removed 73 (35 requested) atoms. Cycle 3: After refmac, R = 0.2690 (Rfree = 0.000) for 10860 atoms. Found 70 (70 requested) and removed 60 (35 requested) atoms. Cycle 4: After refmac, R = 0.2481 (Rfree = 0.000) for 10787 atoms. Found 63 (69 requested) and removed 50 (34 requested) atoms. Cycle 5: After refmac, R = 0.2465 (Rfree = 0.000) for 10717 atoms. Found 69 (69 requested) and removed 51 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 11151 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 11180 seeds are put forward Round 1: 780 peptides, 125 chains. Longest chain 17 peptides. Score 0.426 Round 2: 847 peptides, 116 chains. Longest chain 23 peptides. Score 0.507 Round 3: 884 peptides, 116 chains. Longest chain 23 peptides. Score 0.534 Round 4: 865 peptides, 112 chains. Longest chain 22 peptides. Score 0.533 Round 5: 854 peptides, 99 chains. Longest chain 22 peptides. Score 0.566 Taking the results from Round 5 Chains 106, Residues 755, Estimated correctness of the model 0.9 % 11 chains (101 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 24882 restraints for refining 11249 atoms. 21631 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2678 (Rfree = 0.000) for 11249 atoms. Found 72 (72 requested) and removed 91 (36 requested) atoms. Cycle 7: After refmac, R = 0.2442 (Rfree = 0.000) for 11112 atoms. Found 72 (72 requested) and removed 59 (36 requested) atoms. Cycle 8: After refmac, R = 0.2415 (Rfree = 0.000) for 11022 atoms. Found 71 (71 requested) and removed 62 (35 requested) atoms. Cycle 9: After refmac, R = 0.2056 (Rfree = 0.000) for 10956 atoms. Found 34 (70 requested) and removed 52 (35 requested) atoms. Cycle 10: After refmac, R = 0.2070 (Rfree = 0.000) for 10893 atoms. Found 35 (70 requested) and removed 49 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 11283 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 11302 seeds are put forward Round 1: 756 peptides, 122 chains. Longest chain 16 peptides. Score 0.417 Round 2: 865 peptides, 125 chains. Longest chain 26 peptides. Score 0.491 Round 3: 897 peptides, 118 chains. Longest chain 23 peptides. Score 0.536 Round 4: 889 peptides, 112 chains. Longest chain 27 peptides. Score 0.550 Round 5: 864 peptides, 111 chains. Longest chain 26 peptides. Score 0.536 Taking the results from Round 4 Chains 121, Residues 777, Estimated correctness of the model 0.0 % 13 chains (103 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 24545 restraints for refining 11254 atoms. 21229 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2717 (Rfree = 0.000) for 11254 atoms. Found 72 (72 requested) and removed 82 (36 requested) atoms. Cycle 12: After refmac, R = 0.2301 (Rfree = 0.000) for 11099 atoms. Found 65 (72 requested) and removed 60 (36 requested) atoms. Cycle 13: After refmac, R = 0.2208 (Rfree = 0.000) for 11022 atoms. Found 50 (71 requested) and removed 48 (35 requested) atoms. Cycle 14: After refmac, R = 0.2148 (Rfree = 0.000) for 10958 atoms. Found 44 (70 requested) and removed 61 (35 requested) atoms. Cycle 15: After refmac, R = 0.2084 (Rfree = 0.000) for 10879 atoms. Found 44 (70 requested) and removed 47 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 11239 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 11266 seeds are put forward Round 1: 744 peptides, 126 chains. Longest chain 20 peptides. Score 0.393 Round 2: 845 peptides, 118 chains. Longest chain 26 peptides. Score 0.499 Round 3: 861 peptides, 105 chains. Longest chain 34 peptides. Score 0.552 Round 4: 854 peptides, 108 chains. Longest chain 23 peptides. Score 0.538 Round 5: 853 peptides, 107 chains. Longest chain 46 peptides. Score 0.540 Taking the results from Round 3 Chains 107, Residues 756, Estimated correctness of the model 0.0 % 5 chains (82 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 24524 restraints for refining 11254 atoms. 21275 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2471 (Rfree = 0.000) for 11254 atoms. Found 72 (72 requested) and removed 97 (36 requested) atoms. Cycle 17: After refmac, R = 0.2322 (Rfree = 0.000) for 11129 atoms. Found 72 (72 requested) and removed 61 (36 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2338 (Rfree = 0.000) for 11065 atoms. Found 71 (71 requested) and removed 69 (35 requested) atoms. Cycle 19: After refmac, R = 0.2221 (Rfree = 0.000) for 11018 atoms. Found 63 (71 requested) and removed 49 (35 requested) atoms. Cycle 20: After refmac, R = 0.2224 (Rfree = 0.000) for 11001 atoms. Found 57 (70 requested) and removed 59 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 11366 seeds are put forward NCS extension: 8 residues added (10 deleted due to clashes), 11374 seeds are put forward Round 1: 774 peptides, 125 chains. Longest chain 19 peptides. Score 0.421 Round 2: 839 peptides, 121 chains. Longest chain 20 peptides. Score 0.485 Round 3: 858 peptides, 113 chains. Longest chain 25 peptides. Score 0.525 Round 4: 839 peptides, 110 chains. Longest chain 26 peptides. Score 0.521 Round 5: 867 peptides, 115 chains. Longest chain 27 peptides. Score 0.525 Taking the results from Round 5 Chains 119, Residues 752, Estimated correctness of the model 0.0 % 6 chains (47 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25186 restraints for refining 11254 atoms. 22129 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2518 (Rfree = 0.000) for 11254 atoms. Found 72 (72 requested) and removed 74 (36 requested) atoms. Cycle 22: After refmac, R = 0.2383 (Rfree = 0.000) for 11150 atoms. Found 72 (72 requested) and removed 71 (36 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2517 (Rfree = 0.000) for 11081 atoms. Found 71 (71 requested) and removed 59 (35 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2223 (Rfree = 0.000) for 11002 atoms. Found 71 (71 requested) and removed 61 (35 requested) atoms. Cycle 25: After refmac, R = 0.2193 (Rfree = 0.000) for 10962 atoms. Found 55 (70 requested) and removed 46 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 11353 seeds are put forward NCS extension: 24 residues added (16 deleted due to clashes), 11377 seeds are put forward Round 1: 714 peptides, 125 chains. Longest chain 19 peptides. Score 0.371 Round 2: 803 peptides, 118 chains. Longest chain 21 peptides. Score 0.468 Round 3: 803 peptides, 112 chains. Longest chain 21 peptides. Score 0.488 Round 4: 804 peptides, 116 chains. Longest chain 21 peptides. Score 0.475 Round 5: 809 peptides, 113 chains. Longest chain 19 peptides. Score 0.489 Taking the results from Round 5 Chains 114, Residues 696, Estimated correctness of the model 0.0 % 7 chains (41 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25449 restraints for refining 11255 atoms. 22644 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2754 (Rfree = 0.000) for 11255 atoms. Found 72 (72 requested) and removed 69 (36 requested) atoms. Cycle 27: After refmac, R = 0.2396 (Rfree = 0.000) for 11163 atoms. Found 72 (72 requested) and removed 61 (36 requested) atoms. Cycle 28: After refmac, R = 0.2375 (Rfree = 0.000) for 11107 atoms. Found 71 (71 requested) and removed 62 (35 requested) atoms. Cycle 29: After refmac, R = 0.2643 (Rfree = 0.000) for 11041 atoms. Found 71 (71 requested) and removed 62 (35 requested) atoms. Cycle 30: After refmac, R = 0.2283 (Rfree = 0.000) for 10962 atoms. Found 70 (70 requested) and removed 56 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 11317 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 11330 seeds are put forward Round 1: 702 peptides, 129 chains. Longest chain 20 peptides. Score 0.345 Round 2: 764 peptides, 117 chains. Longest chain 20 peptides. Score 0.441 Round 3: 794 peptides, 123 chains. Longest chain 22 peptides. Score 0.444 Round 4: 788 peptides, 121 chains. Longest chain 23 peptides. Score 0.446 Round 5: 780 peptides, 113 chains. Longest chain 20 peptides. Score 0.467 Taking the results from Round 5 Chains 117, Residues 667, Estimated correctness of the model 0.0 % 9 chains (55 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25523 restraints for refining 11252 atoms. 22792 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2499 (Rfree = 0.000) for 11252 atoms. Found 72 (72 requested) and removed 84 (36 requested) atoms. Cycle 32: After refmac, R = 0.2328 (Rfree = 0.000) for 11156 atoms. Found 72 (72 requested) and removed 62 (36 requested) atoms. Cycle 33: After refmac, R = 0.2291 (Rfree = 0.000) for 11112 atoms. Found 71 (71 requested) and removed 53 (35 requested) atoms. Cycle 34: After refmac, R = 0.2224 (Rfree = 0.000) for 11097 atoms. Found 71 (71 requested) and removed 55 (35 requested) atoms. Cycle 35: After refmac, R = 0.2183 (Rfree = 0.000) for 11076 atoms. Found 53 (71 requested) and removed 56 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 11436 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 11461 seeds are put forward Round 1: 643 peptides, 122 chains. Longest chain 17 peptides. Score 0.319 Round 2: 712 peptides, 116 chains. Longest chain 17 peptides. Score 0.402 Round 3: 723 peptides, 116 chains. Longest chain 18 peptides. Score 0.411 Round 4: 729 peptides, 117 chains. Longest chain 20 peptides. Score 0.413 Round 5: 761 peptides, 113 chains. Longest chain 21 peptides. Score 0.453 Taking the results from Round 5 Chains 115, Residues 648, Estimated correctness of the model 0.0 % 7 chains (43 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25491 restraints for refining 11253 atoms. 22878 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2442 (Rfree = 0.000) for 11253 atoms. Found 72 (72 requested) and removed 53 (36 requested) atoms. Cycle 37: After refmac, R = 0.2286 (Rfree = 0.000) for 11202 atoms. Found 64 (72 requested) and removed 60 (36 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2289 (Rfree = 0.000) for 11142 atoms. Found 71 (71 requested) and removed 57 (35 requested) atoms. Cycle 39: After refmac, R = 0.2270 (Rfree = 0.000) for 11117 atoms. Found 71 (71 requested) and removed 62 (35 requested) atoms. Cycle 40: After refmac, R = 0.1952 (Rfree = 0.000) for 11080 atoms. Found 31 (71 requested) and removed 44 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 11424 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 11457 seeds are put forward Round 1: 613 peptides, 121 chains. Longest chain 12 peptides. Score 0.296 Round 2: 706 peptides, 120 chains. Longest chain 14 peptides. Score 0.382 Round 3: 703 peptides, 113 chains. Longest chain 19 peptides. Score 0.406 Round 4: 694 peptides, 116 chains. Longest chain 15 peptides. Score 0.387 Round 5: 746 peptides, 115 chains. Longest chain 18 peptides. Score 0.434 Taking the results from Round 5 Chains 115, Residues 631, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 22267 reflections ( 99.87 % complete ) and 25569 restraints for refining 11255 atoms. 23091 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2362 (Rfree = 0.000) for 11255 atoms. Found 72 (72 requested) and removed 76 (36 requested) atoms. Cycle 42: After refmac, R = 0.2299 (Rfree = 0.000) for 11179 atoms. Found 72 (72 requested) and removed 68 (36 requested) atoms. Cycle 43: After refmac, R = 0.1921 (Rfree = 0.000) for 11137 atoms. Found 23 (71 requested) and removed 39 (35 requested) atoms. Cycle 44: After refmac, R = 0.1860 (Rfree = 0.000) for 11093 atoms. Found 24 (71 requested) and removed 43 (35 requested) atoms. Cycle 45: After refmac, R = 0.1806 (Rfree = 0.000) for 11056 atoms. Found 10 (71 requested) and removed 41 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 11392 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 11408 seeds are put forward Round 1: 619 peptides, 121 chains. Longest chain 16 peptides. Score 0.301 Round 2: 705 peptides, 121 chains. Longest chain 15 peptides. Score 0.378 Round 3: 732 peptides, 123 chains. Longest chain 18 peptides. Score 0.393 Round 4: 714 peptides, 119 chains. Longest chain 15 peptides. Score 0.393 Round 5: 718 peptides, 114 chains. Longest chain 21 peptides. Score 0.415 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 115, Residues 604, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input Building loops using Loopy2018 115 chains (604 residues) following loop building 4 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22267 reflections ( 99.87 % complete ) and 25777 restraints for refining 11253 atoms. 23384 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2513 (Rfree = 0.000) for 11253 atoms. Found 0 (72 requested) and removed 36 (36 requested) atoms. Cycle 47: After refmac, R = 0.2287 (Rfree = 0.000) for 11148 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.2397 (Rfree = 0.000) for 11074 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2266 (Rfree = 0.000) for 11005 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Writing output files ... TimeTaking 124.2