Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl6-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:06 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/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-hancs/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-hancs.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-hancs.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 13852 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3301 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3312 (Rfree = 0.000) for 13852 atoms. Found 88 (88 requested) and removed 75 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.28 Search for helices and strands: 0 residues in 0 chains, 14129 seeds are put forward NCS extension: 0 residues added, 14129 seeds are put forward Round 1: 581 peptides, 108 chains. Longest chain 17 peptides. Score 0.318 Round 2: 750 peptides, 107 chains. Longest chain 20 peptides. Score 0.465 Round 3: 814 peptides, 110 chains. Longest chain 27 peptides. Score 0.503 Round 4: 842 peptides, 109 chains. Longest chain 24 peptides. Score 0.526 Round 5: 835 peptides, 106 chains. Longest chain 30 peptides. Score 0.531 Taking the results from Round 5 Chains 111, Residues 729, Estimated correctness of the model 0.0 % 10 chains (101 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25263 restraints for refining 11248 atoms. 22113 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2991 (Rfree = 0.000) for 11248 atoms. Found 72 (72 requested) and removed 93 (36 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2754 (Rfree = 0.000) for 10960 atoms. Found 72 (72 requested) and removed 67 (36 requested) atoms. Cycle 3: After refmac, R = 0.2729 (Rfree = 0.000) for 10778 atoms. Found 70 (70 requested) and removed 62 (35 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2607 (Rfree = 0.000) for 10684 atoms. Found 66 (69 requested) and removed 59 (34 requested) atoms. Cycle 5: After refmac, R = 0.2573 (Rfree = 0.000) for 10595 atoms. Found 67 (68 requested) and removed 61 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 10994 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 11026 seeds are put forward Round 1: 736 peptides, 128 chains. Longest chain 17 peptides. Score 0.378 Round 2: 846 peptides, 117 chains. Longest chain 24 peptides. Score 0.503 Round 3: 851 peptides, 109 chains. Longest chain 29 peptides. Score 0.533 Round 4: 840 peptides, 108 chains. Longest chain 23 peptides. Score 0.528 Round 5: 867 peptides, 108 chains. Longest chain 25 peptides. Score 0.547 Taking the results from Round 5 Chains 114, Residues 759, Estimated correctness of the model 0.0 % 7 chains (79 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 24558 restraints for refining 11089 atoms. 21357 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2755 (Rfree = 0.000) for 11089 atoms. Found 71 (71 requested) and removed 95 (35 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2592 (Rfree = 0.000) for 10897 atoms. Found 66 (70 requested) and removed 78 (35 requested) atoms. Cycle 8: After refmac, R = 0.2460 (Rfree = 0.000) for 10758 atoms. Found 50 (69 requested) and removed 61 (34 requested) atoms. Cycle 9: After refmac, R = 0.2428 (Rfree = 0.000) for 10667 atoms. Found 49 (68 requested) and removed 56 (34 requested) atoms. Cycle 10: After refmac, R = 0.2429 (Rfree = 0.000) for 10590 atoms. Found 68 (68 requested) and removed 53 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 10946 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 10964 seeds are put forward Round 1: 697 peptides, 119 chains. Longest chain 17 peptides. Score 0.378 Round 2: 828 peptides, 118 chains. Longest chain 21 peptides. Score 0.487 Round 3: 836 peptides, 116 chains. Longest chain 27 peptides. Score 0.499 Round 4: 849 peptides, 114 chains. Longest chain 39 peptides. Score 0.515 Round 5: 827 peptides, 109 chains. Longest chain 29 peptides. Score 0.516 Taking the results from Round 5 Chains 112, Residues 718, Estimated correctness of the model 0.0 % 8 chains (93 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 24914 restraints for refining 11254 atoms. 21815 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2649 (Rfree = 0.000) for 11254 atoms. Found 72 (72 requested) and removed 97 (36 requested) atoms. Cycle 12: After refmac, R = 0.2541 (Rfree = 0.000) for 11095 atoms. Found 72 (72 requested) and removed 92 (36 requested) atoms. Cycle 13: After refmac, R = 0.2467 (Rfree = 0.000) for 10981 atoms. Found 71 (71 requested) and removed 56 (35 requested) atoms. Cycle 14: After refmac, R = 0.2370 (Rfree = 0.000) for 10925 atoms. Found 54 (70 requested) and removed 54 (35 requested) atoms. Cycle 15: After refmac, R = 0.2438 (Rfree = 0.000) for 10849 atoms. Found 69 (70 requested) and removed 51 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 11260 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 11283 seeds are put forward Round 1: 710 peptides, 124 chains. Longest chain 16 peptides. Score 0.371 Round 2: 820 peptides, 114 chains. Longest chain 28 peptides. Score 0.494 Round 3: 820 peptides, 123 chains. Longest chain 17 peptides. Score 0.464 Round 4: 847 peptides, 123 chains. Longest chain 19 peptides. Score 0.484 Round 5: 849 peptides, 121 chains. Longest chain 20 peptides. Score 0.493 Taking the results from Round 2 Chains 115, Residues 706, Estimated correctness of the model 0.0 % 6 chains (74 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 23330 restraints for refining 10927 atoms. 20337 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2635 (Rfree = 0.000) for 10927 atoms. Found 70 (70 requested) and removed 98 (35 requested) atoms. Cycle 17: After refmac, R = 0.2511 (Rfree = 0.000) for 10802 atoms. Found 69 (69 requested) and removed 59 (34 requested) atoms. Cycle 18: After refmac, R = 0.2312 (Rfree = 0.000) for 10741 atoms. Found 69 (69 requested) and removed 63 (34 requested) atoms. Cycle 19: After refmac, R = 0.2352 (Rfree = 0.000) for 10687 atoms. Found 68 (68 requested) and removed 62 (34 requested) atoms. Cycle 20: After refmac, R = 0.2263 (Rfree = 0.000) for 10644 atoms. Found 68 (68 requested) and removed 68 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 10989 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 11020 seeds are put forward Round 1: 726 peptides, 133 chains. Longest chain 17 peptides. Score 0.351 Round 2: 814 peptides, 128 chains. Longest chain 19 peptides. Score 0.442 Round 3: 802 peptides, 121 chains. Longest chain 18 peptides. Score 0.457 Round 4: 794 peptides, 113 chains. Longest chain 21 peptides. Score 0.478 Round 5: 791 peptides, 110 chains. Longest chain 22 peptides. Score 0.486 Taking the results from Round 5 Chains 112, Residues 681, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25665 restraints for refining 11253 atoms. 22980 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2711 (Rfree = 0.000) for 11253 atoms. Found 72 (72 requested) and removed 96 (36 requested) atoms. Cycle 22: After refmac, R = 0.2428 (Rfree = 0.000) for 11112 atoms. Found 72 (72 requested) and removed 66 (36 requested) atoms. Cycle 23: After refmac, R = 0.2344 (Rfree = 0.000) for 11050 atoms. Found 71 (71 requested) and removed 55 (35 requested) atoms. Cycle 24: After refmac, R = 0.2355 (Rfree = 0.000) for 11003 atoms. Found 70 (70 requested) and removed 47 (35 requested) atoms. Cycle 25: After refmac, R = 0.2286 (Rfree = 0.000) for 10971 atoms. Found 70 (70 requested) and removed 58 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 11349 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 11376 seeds are put forward Round 1: 639 peptides, 122 chains. Longest chain 17 peptides. Score 0.316 Round 2: 753 peptides, 122 chains. Longest chain 16 peptides. Score 0.414 Round 3: 776 peptides, 114 chains. Longest chain 24 peptides. Score 0.461 Round 4: 769 peptides, 112 chains. Longest chain 22 peptides. Score 0.462 Round 5: 784 peptides, 117 chains. Longest chain 21 peptides. Score 0.457 Taking the results from Round 4 Chains 114, Residues 657, Estimated correctness of the model 0.0 % 11 chains (62 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 22267 reflections ( 99.87 % complete ) and 25462 restraints for refining 11255 atoms. 22784 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2491 (Rfree = 0.000) for 11255 atoms. Found 50 (72 requested) and removed 80 (36 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2461 (Rfree = 0.000) for 11152 atoms. Found 72 (72 requested) and removed 75 (36 requested) atoms. Cycle 28: After refmac, R = 0.2502 (Rfree = 0.000) for 11090 atoms. Found 71 (71 requested) and removed 70 (35 requested) atoms. Cycle 29: After refmac, R = 0.2331 (Rfree = 0.000) for 11044 atoms. Found 71 (71 requested) and removed 60 (35 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2013 (Rfree = 0.000) for 11017 atoms. Found 19 (70 requested) and removed 48 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 11332 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 11345 seeds are put forward Round 1: 697 peptides, 138 chains. Longest chain 17 peptides. Score 0.307 Round 2: 740 peptides, 123 chains. Longest chain 14 peptides. Score 0.400 Round 3: 787 peptides, 125 chains. Longest chain 19 peptides. Score 0.431 Round 4: 772 peptides, 117 chains. Longest chain 21 peptides. Score 0.447 Round 5: 764 peptides, 122 chains. Longest chain 20 peptides. Score 0.423 Taking the results from Round 4 Chains 120, Residues 655, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25762 restraints for refining 11255 atoms. 23156 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2513 (Rfree = 0.000) for 11255 atoms. Found 72 (72 requested) and removed 69 (36 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2460 (Rfree = 0.000) for 11197 atoms. Found 72 (72 requested) and removed 58 (36 requested) atoms. Cycle 33: After refmac, R = 0.2373 (Rfree = 0.000) for 11157 atoms. Found 71 (71 requested) and removed 57 (35 requested) atoms. Cycle 34: After refmac, R = 0.2403 (Rfree = 0.000) for 11123 atoms. Found 71 (71 requested) and removed 64 (35 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2421 (Rfree = 0.000) for 11097 atoms. Found 71 (71 requested) and removed 57 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 11512 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 11524 seeds are put forward Round 1: 598 peptides, 118 chains. Longest chain 11 peptides. Score 0.294 Round 2: 706 peptides, 123 chains. Longest chain 18 peptides. Score 0.371 Round 3: 718 peptides, 115 chains. Longest chain 21 peptides. Score 0.411 Round 4: 722 peptides, 118 chains. Longest chain 23 peptides. Score 0.403 Round 5: 728 peptides, 115 chains. Longest chain 23 peptides. Score 0.419 Taking the results from Round 5 Chains 118, Residues 613, Estimated correctness of the model 0.0 % 8 chains (47 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25770 restraints for refining 11253 atoms. 23298 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2488 (Rfree = 0.000) for 11253 atoms. Found 72 (72 requested) and removed 67 (36 requested) atoms. Cycle 37: After refmac, R = 0.2403 (Rfree = 0.000) for 11173 atoms. Found 72 (72 requested) and removed 62 (36 requested) atoms. Cycle 38: After refmac, R = 0.2329 (Rfree = 0.000) for 11123 atoms. Found 71 (71 requested) and removed 55 (35 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1977 (Rfree = 0.000) for 11086 atoms. Found 25 (71 requested) and removed 44 (35 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1901 (Rfree = 0.000) for 11033 atoms. Found 20 (71 requested) and removed 40 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.17 Search for helices and strands: 0 residues in 0 chains, 11400 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11417 seeds are put forward Round 1: 569 peptides, 116 chains. Longest chain 11 peptides. Score 0.274 Round 2: 671 peptides, 110 chains. Longest chain 16 peptides. Score 0.390 Round 3: 699 peptides, 117 chains. Longest chain 25 peptides. Score 0.388 Round 4: 672 peptides, 101 chains. Longest chain 20 peptides. Score 0.424 Round 5: 662 peptides, 105 chains. Longest chain 25 peptides. Score 0.401 Taking the results from Round 4 Chains 102, Residues 571, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25826 restraints for refining 11254 atoms. 23543 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2376 (Rfree = 0.000) for 11254 atoms. Found 72 (72 requested) and removed 51 (36 requested) atoms. Cycle 42: After refmac, R = 0.2396 (Rfree = 0.000) for 11221 atoms. Found 72 (72 requested) and removed 57 (36 requested) atoms. Cycle 43: After refmac, R = 0.2378 (Rfree = 0.000) for 11187 atoms. Found 72 (72 requested) and removed 50 (36 requested) atoms. Cycle 44: After refmac, R = 0.2316 (Rfree = 0.000) for 11163 atoms. Found 71 (71 requested) and removed 48 (35 requested) atoms. Cycle 45: After refmac, R = 0.2350 (Rfree = 0.000) for 11145 atoms. Found 71 (71 requested) and removed 49 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 11530 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 11553 seeds are put forward Round 1: 503 peptides, 108 chains. Longest chain 8 peptides. Score 0.242 Round 2: 613 peptides, 107 chains. Longest chain 20 peptides. Score 0.351 Round 3: 619 peptides, 107 chains. Longest chain 14 peptides. Score 0.356 Round 4: 644 peptides, 109 chains. Longest chain 16 peptides. Score 0.370 Round 5: 632 peptides, 101 chains. Longest chain 21 peptides. Score 0.391 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 101, Residues 531, Estimated correctness of the model 0.0 % 3 chains (25 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 101 chains (531 residues) following loop building 3 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22267 reflections ( 99.87 % complete ) and 25821 restraints for refining 11173 atoms. 23713 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2637 (Rfree = 0.000) for 11173 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.2490 (Rfree = 0.000) for 11060 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.2584 (Rfree = 0.000) for 10968 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.2571 (Rfree = 0.000) for 10886 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Writing output files ... TimeTaking 161.42