null Sun 23 Dec 22:22:49 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 1vl6-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-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/1vl6-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-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 ============================================================ Sun 23 Dec 22:22:59 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/1vl6-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.8-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 1214 and 0 Target number of residues in the AU: 1214 Target solvent content: 0.6639 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: 1vl6-3.8-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: 1vl6-3.8-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 3.800 Wilson plot Bfac: 87.74 18938 reflections ( 99.85 % complete ) and 0 restraints for refining 13824 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3383 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3324 (Rfree = 0.000) for 13824 atoms. Found 76 (76 requested) and removed 86 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 14075 seeds are put forward NCS extension: 0 residues added, 14075 seeds are put forward Round 1: 581 peptides, 106 chains. Longest chain 15 peptides. Score 0.326 Round 2: 715 peptides, 107 chains. Longest chain 19 peptides. Score 0.437 Round 3: 788 peptides, 102 chains. Longest chain 31 peptides. Score 0.511 Round 4: 819 peptides, 108 chains. Longest chain 28 peptides. Score 0.513 Round 5: 815 peptides, 100 chains. Longest chain 28 peptides. Score 0.536 Taking the results from Round 5 Chains 104, Residues 715, Estimated correctness of the model 0.0 % 16 chains (140 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 24949 restraints for refining 11222 atoms. 21747 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2856 (Rfree = 0.000) for 11222 atoms. Found 58 (61 requested) and removed 97 (30 requested) atoms. Cycle 2: After refmac, R = 0.2659 (Rfree = 0.000) for 10891 atoms. Found 61 (61 requested) and removed 85 (30 requested) atoms. Cycle 3: After refmac, R = 0.2577 (Rfree = 0.000) for 10701 atoms. Found 55 (59 requested) and removed 60 (29 requested) atoms. Cycle 4: After refmac, R = 0.2427 (Rfree = 0.000) for 10580 atoms. Found 57 (58 requested) and removed 65 (29 requested) atoms. Cycle 5: After refmac, R = 0.2359 (Rfree = 0.000) for 10490 atoms. Found 58 (58 requested) and removed 61 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 10832 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 10849 seeds are put forward Round 1: 736 peptides, 121 chains. Longest chain 19 peptides. Score 0.404 Round 2: 794 peptides, 110 chains. Longest chain 25 peptides. Score 0.488 Round 3: 806 peptides, 103 chains. Longest chain 27 peptides. Score 0.520 Round 4: 805 peptides, 106 chains. Longest chain 21 peptides. Score 0.510 Round 5: 831 peptides, 106 chains. Longest chain 28 peptides. Score 0.528 Taking the results from Round 5 Chains 107, Residues 725, Estimated correctness of the model 0.0 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 24716 restraints for refining 10977 atoms. 21800 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2565 (Rfree = 0.000) for 10977 atoms. Found 60 (60 requested) and removed 99 (30 requested) atoms. Cycle 7: After refmac, R = 0.2440 (Rfree = 0.000) for 10765 atoms. Found 60 (60 requested) and removed 68 (30 requested) atoms. Cycle 8: After refmac, R = 0.2388 (Rfree = 0.000) for 10596 atoms. Found 59 (59 requested) and removed 53 (29 requested) atoms. Cycle 9: After refmac, R = 0.1975 (Rfree = 0.000) for 10523 atoms. Found 25 (58 requested) and removed 41 (29 requested) atoms. Cycle 10: After refmac, R = 0.2191 (Rfree = 0.000) for 10451 atoms. Found 57 (57 requested) and removed 47 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 10865 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 10884 seeds are put forward Round 1: 732 peptides, 124 chains. Longest chain 23 peptides. Score 0.390 Round 2: 820 peptides, 116 chains. Longest chain 25 peptides. Score 0.488 Round 3: 837 peptides, 111 chains. Longest chain 24 peptides. Score 0.516 Round 4: 844 peptides, 112 chains. Longest chain 27 peptides. Score 0.518 Round 5: 840 peptides, 115 chains. Longest chain 21 peptides. Score 0.506 Taking the results from Round 4 Chains 115, Residues 732, Estimated correctness of the model 0.0 % 9 chains (82 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 24324 restraints for refining 11141 atoms. 21212 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2600 (Rfree = 0.000) for 11141 atoms. Found 61 (61 requested) and removed 100 (30 requested) atoms. Cycle 12: After refmac, R = 0.2420 (Rfree = 0.000) for 10957 atoms. Found 58 (61 requested) and removed 57 (30 requested) atoms. Cycle 13: After refmac, R = 0.2326 (Rfree = 0.000) for 10842 atoms. Found 57 (60 requested) and removed 56 (30 requested) atoms. Cycle 14: After refmac, R = 0.2240 (Rfree = 0.000) for 10769 atoms. Found 38 (59 requested) and removed 53 (29 requested) atoms. Cycle 15: After refmac, R = 0.1944 (Rfree = 0.000) for 10687 atoms. Found 19 (59 requested) and removed 42 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 11010 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 11036 seeds are put forward Round 1: 712 peptides, 126 chains. Longest chain 22 peptides. Score 0.365 Round 2: 815 peptides, 117 chains. Longest chain 18 peptides. Score 0.480 Round 3: 834 peptides, 119 chains. Longest chain 18 peptides. Score 0.488 Round 4: 853 peptides, 123 chains. Longest chain 18 peptides. Score 0.489 Round 5: 816 peptides, 111 chains. Longest chain 21 peptides. Score 0.501 Taking the results from Round 5 Chains 115, Residues 705, Estimated correctness of the model 0.0 % 10 chains (68 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25129 restraints for refining 11229 atoms. 22182 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2659 (Rfree = 0.000) for 11229 atoms. Found 61 (61 requested) and removed 105 (30 requested) atoms. Cycle 17: After refmac, R = 0.2446 (Rfree = 0.000) for 11081 atoms. Found 61 (61 requested) and removed 82 (30 requested) atoms. Cycle 18: After refmac, R = 0.2363 (Rfree = 0.000) for 10989 atoms. Found 60 (60 requested) and removed 64 (30 requested) atoms. Cycle 19: After refmac, R = 0.2333 (Rfree = 0.000) for 10917 atoms. Found 60 (60 requested) and removed 60 (30 requested) atoms. Cycle 20: After refmac, R = 0.1942 (Rfree = 0.000) for 10866 atoms. Found 26 (60 requested) and removed 45 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 11191 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 11216 seeds are put forward Round 1: 710 peptides, 131 chains. Longest chain 17 peptides. Score 0.345 Round 2: 769 peptides, 115 chains. Longest chain 19 peptides. Score 0.452 Round 3: 787 peptides, 113 chains. Longest chain 26 peptides. Score 0.473 Round 4: 794 peptides, 112 chains. Longest chain 19 peptides. Score 0.482 Round 5: 809 peptides, 113 chains. Longest chain 21 peptides. Score 0.489 Taking the results from Round 5 Chains 113, Residues 696, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25323 restraints for refining 11231 atoms. 22532 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2591 (Rfree = 0.000) for 11231 atoms. Found 61 (61 requested) and removed 82 (30 requested) atoms. Cycle 22: After refmac, R = 0.2323 (Rfree = 0.000) for 11096 atoms. Found 61 (61 requested) and removed 55 (30 requested) atoms. Cycle 23: After refmac, R = 0.2269 (Rfree = 0.000) for 11014 atoms. Found 61 (61 requested) and removed 56 (30 requested) atoms. Cycle 24: After refmac, R = 0.2221 (Rfree = 0.000) for 10965 atoms. Found 60 (60 requested) and removed 44 (30 requested) atoms. Cycle 25: After refmac, R = 0.2229 (Rfree = 0.000) for 10938 atoms. Found 60 (60 requested) and removed 47 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 11259 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 11283 seeds are put forward Round 1: 637 peptides, 126 chains. Longest chain 15 peptides. Score 0.298 Round 2: 703 peptides, 105 chains. Longest chain 20 peptides. Score 0.435 Round 3: 703 peptides, 110 chains. Longest chain 19 peptides. Score 0.417 Round 4: 729 peptides, 113 chains. Longest chain 15 peptides. Score 0.427 Round 5: 740 peptides, 112 chains. Longest chain 19 peptides. Score 0.440 Taking the results from Round 5 Chains 116, Residues 628, Estimated correctness of the model 0.0 % 8 chains (50 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25582 restraints for refining 11230 atoms. 23039 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2533 (Rfree = 0.000) for 11230 atoms. Found 61 (61 requested) and removed 68 (30 requested) atoms. Cycle 27: After refmac, R = 0.2338 (Rfree = 0.000) for 11137 atoms. Found 61 (61 requested) and removed 88 (30 requested) atoms. Cycle 28: After refmac, R = 0.1945 (Rfree = 0.000) for 11045 atoms. Found 54 (61 requested) and removed 52 (30 requested) atoms. Cycle 29: After refmac, R = 0.1882 (Rfree = 0.000) for 11011 atoms. Found 25 (60 requested) and removed 45 (30 requested) atoms. Cycle 30: After refmac, R = 0.1860 (Rfree = 0.000) for 10969 atoms. Found 30 (60 requested) and removed 39 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 11333 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 11352 seeds are put forward Round 1: 679 peptides, 137 chains. Longest chain 14 peptides. Score 0.294 Round 2: 741 peptides, 123 chains. Longest chain 16 peptides. Score 0.401 Round 3: 764 peptides, 123 chains. Longest chain 17 peptides. Score 0.420 Round 4: 766 peptides, 120 chains. Longest chain 18 peptides. Score 0.432 Round 5: 766 peptides, 116 chains. Longest chain 17 peptides. Score 0.446 Taking the results from Round 5 Chains 118, Residues 650, Estimated correctness of the model 0.0 % 6 chains (41 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25794 restraints for refining 11230 atoms. 23179 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2584 (Rfree = 0.000) for 11230 atoms. Found 61 (61 requested) and removed 75 (30 requested) atoms. Cycle 32: After refmac, R = 0.2334 (Rfree = 0.000) for 11113 atoms. Found 61 (61 requested) and removed 55 (30 requested) atoms. Cycle 33: After refmac, R = 0.1965 (Rfree = 0.000) for 11042 atoms. Found 28 (61 requested) and removed 41 (30 requested) atoms. Cycle 34: After refmac, R = 0.1867 (Rfree = 0.000) for 10990 atoms. Found 12 (60 requested) and removed 39 (30 requested) atoms. Cycle 35: After refmac, R = 0.1844 (Rfree = 0.000) for 10948 atoms. Found 10 (60 requested) and removed 35 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 11320 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 11335 seeds are put forward Round 1: 650 peptides, 128 chains. Longest chain 15 peptides. Score 0.303 Round 2: 718 peptides, 120 chains. Longest chain 20 peptides. Score 0.393 Round 3: 733 peptides, 121 chains. Longest chain 16 peptides. Score 0.401 Round 4: 731 peptides, 119 chains. Longest chain 17 peptides. Score 0.407 Round 5: 723 peptides, 111 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 5 Chains 111, Residues 612, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 25896 restraints for refining 11230 atoms. 23447 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2478 (Rfree = 0.000) for 11230 atoms. Found 61 (61 requested) and removed 51 (30 requested) atoms. Cycle 37: After refmac, R = 0.2411 (Rfree = 0.000) for 11188 atoms. Found 61 (61 requested) and removed 60 (30 requested) atoms. Cycle 38: After refmac, R = 0.2269 (Rfree = 0.000) for 11147 atoms. Found 61 (61 requested) and removed 66 (30 requested) atoms. Cycle 39: After refmac, R = 0.2355 (Rfree = 0.000) for 11103 atoms. Found 61 (61 requested) and removed 49 (30 requested) atoms. Cycle 40: After refmac, R = 0.2332 (Rfree = 0.000) for 11066 atoms. Found 61 (61 requested) and removed 46 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 11394 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 11411 seeds are put forward Round 1: 518 peptides, 108 chains. Longest chain 10 peptides. Score 0.257 Round 2: 639 peptides, 120 chains. Longest chain 15 peptides. Score 0.324 Round 3: 648 peptides, 115 chains. Longest chain 12 peptides. Score 0.351 Round 4: 662 peptides, 112 chains. Longest chain 15 peptides. Score 0.375 Round 5: 678 peptides, 115 chains. Longest chain 18 peptides. Score 0.377 Taking the results from Round 5 Chains 115, Residues 563, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 18938 reflections ( 99.85 % complete ) and 26298 restraints for refining 11229 atoms. 24099 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2539 (Rfree = 0.000) for 11229 atoms. Found 61 (61 requested) and removed 71 (30 requested) atoms. Cycle 42: After refmac, R = 0.2468 (Rfree = 0.000) for 11142 atoms. Found 61 (61 requested) and removed 53 (30 requested) atoms. Cycle 43: After refmac, R = 0.2341 (Rfree = 0.000) for 11069 atoms. Found 61 (61 requested) and removed 46 (30 requested) atoms. Cycle 44: After refmac, R = 0.2422 (Rfree = 0.000) for 11055 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. Cycle 45: After refmac, R = 0.2231 (Rfree = 0.000) for 11023 atoms. Found 60 (60 requested) and removed 51 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 11455 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 11474 seeds are put forward Round 1: 495 peptides, 108 chains. Longest chain 9 peptides. Score 0.234 Round 2: 616 peptides, 117 chains. Longest chain 13 peptides. Score 0.314 Round 3: 587 peptides, 104 chains. Longest chain 13 peptides. Score 0.339 Round 4: 603 peptides, 103 chains. Longest chain 13 peptides. Score 0.358 Round 5: 608 peptides, 102 chains. Longest chain 14 peptides. Score 0.366 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 102, Residues 506, 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 102 chains (506 residues) following loop building 3 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18938 reflections ( 99.85 % complete ) and 25532 restraints for refining 11030 atoms. 23525 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2527 (Rfree = 0.000) for 11030 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 47: After refmac, R = 0.2357 (Rfree = 0.000) for 10939 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 48: After refmac, R = 0.2038 (Rfree = 0.000) for 10861 atoms. Found 0 (59 requested) and removed 29 (29 requested) atoms. Cycle 49: After refmac, R = 0.1979 (Rfree = 0.000) for 10806 atoms. Found 0 (59 requested) and removed 29 (29 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:35:58 GMT 2018 Job finished. TimeTaking 133.15 Used memory is bytes: 19246504