Sun 23 Dec 23:46:40 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 1vl6-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-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/1vl6-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-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 ============================================================ Sun 23 Dec 23:46:44 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/1vl6-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-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 1343 and 0 Target number of residues in the AU: 1343 Target solvent content: 0.6282 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: 1vl6-3.2-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: 1vl6-3.2-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 3.200 Wilson plot Bfac: 65.59 31643 reflections ( 99.89 % complete ) and 0 restraints for refining 13724 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3279 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2983 (Rfree = 0.000) for 13724 atoms. Found 123 (123 requested) and removed 105 (61 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.90 Search for helices and strands: 0 residues in 0 chains, 14006 seeds are put forward NCS extension: 0 residues added, 14006 seeds are put forward Round 1: 785 peptides, 131 chains. Longest chain 20 peptides. Score 0.408 Round 2: 942 peptides, 117 chains. Longest chain 26 peptides. Score 0.570 Round 3: 998 peptides, 110 chains. Longest chain 43 peptides. Score 0.624 Round 4: 1032 peptides, 113 chains. Longest chain 32 peptides. Score 0.636 Round 5: 1046 peptides, 113 chains. Longest chain 46 peptides. Score 0.644 Taking the results from Round 5 Chains 126, Residues 933, Estimated correctness of the model 52.4 % 21 chains (312 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 21635 restraints for refining 11326 atoms. 16825 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2788 (Rfree = 0.000) for 11326 atoms. Found 98 (101 requested) and removed 106 (50 requested) atoms. Cycle 2: After refmac, R = 0.2644 (Rfree = 0.000) for 11107 atoms. Found 70 (101 requested) and removed 76 (50 requested) atoms. Cycle 3: After refmac, R = 0.2567 (Rfree = 0.000) for 11001 atoms. Found 52 (99 requested) and removed 73 (49 requested) atoms. Cycle 4: After refmac, R = 0.2458 (Rfree = 0.000) for 10922 atoms. Found 43 (98 requested) and removed 64 (49 requested) atoms. Cycle 5: After refmac, R = 0.2459 (Rfree = 0.000) for 10860 atoms. Found 57 (97 requested) and removed 67 (48 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 2.89 Search for helices and strands: 0 residues in 0 chains, 11230 seeds are put forward NCS extension: 22 residues added (22 deleted due to clashes), 11252 seeds are put forward Round 1: 955 peptides, 117 chains. Longest chain 44 peptides. Score 0.578 Round 2: 1032 peptides, 108 chains. Longest chain 35 peptides. Score 0.649 Round 3: 1036 peptides, 99 chains. Longest chain 37 peptides. Score 0.674 Round 4: 1052 peptides, 100 chains. Longest chain 32 peptides. Score 0.680 Round 5: 1044 peptides, 103 chains. Longest chain 34 peptides. Score 0.668 Taking the results from Round 4 Chains 113, Residues 952, Estimated correctness of the model 60.8 % 20 chains (323 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 21537 restraints for refining 11335 atoms. 16582 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2640 (Rfree = 0.000) for 11335 atoms. Found 101 (101 requested) and removed 98 (50 requested) atoms. Cycle 7: After refmac, R = 0.2466 (Rfree = 0.000) for 11237 atoms. Found 46 (101 requested) and removed 79 (50 requested) atoms. Cycle 8: After refmac, R = 0.2336 (Rfree = 0.000) for 11138 atoms. Found 42 (100 requested) and removed 64 (50 requested) atoms. Cycle 9: After refmac, R = 0.2284 (Rfree = 0.000) for 11054 atoms. Found 31 (99 requested) and removed 53 (49 requested) atoms. Cycle 10: After refmac, R = 0.2232 (Rfree = 0.000) for 10989 atoms. Found 39 (99 requested) and removed 62 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 11334 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 11352 seeds are put forward Round 1: 965 peptides, 120 chains. Longest chain 38 peptides. Score 0.576 Round 2: 1034 peptides, 107 chains. Longest chain 33 peptides. Score 0.653 Round 3: 1063 peptides, 98 chains. Longest chain 51 peptides. Score 0.691 Round 4: 1056 peptides, 106 chains. Longest chain 55 peptides. Score 0.667 Round 5: 1065 peptides, 96 chains. Longest chain 50 peptides. Score 0.696 Taking the results from Round 5 Chains 106, Residues 969, Estimated correctness of the model 64.3 % 20 chains (383 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 20906 restraints for refining 11333 atoms. 15678 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2693 (Rfree = 0.000) for 11333 atoms. Found 83 (101 requested) and removed 93 (50 requested) atoms. Cycle 12: After refmac, R = 0.2607 (Rfree = 0.000) for 11254 atoms. Found 56 (101 requested) and removed 78 (50 requested) atoms. Cycle 13: After refmac, R = 0.2362 (Rfree = 0.000) for 11185 atoms. Found 31 (100 requested) and removed 63 (50 requested) atoms. Cycle 14: After refmac, R = 0.2266 (Rfree = 0.000) for 11137 atoms. Found 41 (100 requested) and removed 71 (50 requested) atoms. Cycle 15: After refmac, R = 0.2190 (Rfree = 0.000) for 11084 atoms. Found 22 (99 requested) and removed 65 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.86 Search for helices and strands: 0 residues in 0 chains, 11446 seeds are put forward NCS extension: 20 residues added (21 deleted due to clashes), 11466 seeds are put forward Round 1: 949 peptides, 114 chains. Longest chain 41 peptides. Score 0.583 Round 2: 1052 peptides, 96 chains. Longest chain 47 peptides. Score 0.690 Round 3: 1046 peptides, 109 chains. Longest chain 36 peptides. Score 0.654 Round 4: 1040 peptides, 97 chains. Longest chain 49 peptides. Score 0.681 Round 5: 1038 peptides, 109 chains. Longest chain 42 peptides. Score 0.650 Taking the results from Round 2 Chains 117, Residues 956, Estimated correctness of the model 63.0 % 24 chains (384 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 20616 restraints for refining 11335 atoms. 15452 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2492 (Rfree = 0.000) for 11335 atoms. Found 99 (101 requested) and removed 92 (50 requested) atoms. Cycle 17: After refmac, R = 0.2295 (Rfree = 0.000) for 11287 atoms. Found 34 (101 requested) and removed 71 (50 requested) atoms. Cycle 18: After refmac, R = 0.2343 (Rfree = 0.000) for 11211 atoms. Found 53 (100 requested) and removed 62 (50 requested) atoms. Cycle 19: After refmac, R = 0.2180 (Rfree = 0.000) for 11173 atoms. Found 29 (100 requested) and removed 60 (50 requested) atoms. Cycle 20: After refmac, R = 0.2368 (Rfree = 0.000) for 11125 atoms. Found 76 (99 requested) and removed 56 (49 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 11526 seeds are put forward NCS extension: 11 residues added (7 deleted due to clashes), 11537 seeds are put forward Round 1: 897 peptides, 114 chains. Longest chain 27 peptides. Score 0.549 Round 2: 950 peptides, 93 chains. Longest chain 37 peptides. Score 0.643 Round 3: 949 peptides, 95 chains. Longest chain 37 peptides. Score 0.637 Round 4: 964 peptides, 99 chains. Longest chain 41 peptides. Score 0.635 Round 5: 958 peptides, 101 chains. Longest chain 39 peptides. Score 0.626 Taking the results from Round 2 Chains 99, Residues 857, Estimated correctness of the model 52.1 % 17 chains (279 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22122 restraints for refining 11335 atoms. 17723 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2478 (Rfree = 0.000) for 11335 atoms. Found 75 (101 requested) and removed 77 (50 requested) atoms. Cycle 22: After refmac, R = 0.2228 (Rfree = 0.000) for 11291 atoms. Found 35 (101 requested) and removed 63 (50 requested) atoms. Cycle 23: After refmac, R = 0.2409 (Rfree = 0.000) for 11248 atoms. Found 68 (101 requested) and removed 67 (50 requested) atoms. Cycle 24: After refmac, R = 0.2126 (Rfree = 0.000) for 11221 atoms. Found 31 (100 requested) and removed 66 (50 requested) atoms. Cycle 25: After refmac, R = 0.2093 (Rfree = 0.000) for 11164 atoms. Found 26 (100 requested) and removed 53 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 2.90 Search for helices and strands: 0 residues in 0 chains, 11500 seeds are put forward NCS extension: 4 residues added (24 deleted due to clashes), 11504 seeds are put forward Round 1: 872 peptides, 109 chains. Longest chain 29 peptides. Score 0.547 Round 2: 926 peptides, 98 chains. Longest chain 34 peptides. Score 0.615 Round 3: 954 peptides, 104 chains. Longest chain 35 peptides. Score 0.615 Round 4: 975 peptides, 91 chains. Longest chain 37 peptides. Score 0.662 Round 5: 976 peptides, 101 chains. Longest chain 29 peptides. Score 0.636 Taking the results from Round 4 Chains 97, Residues 884, Estimated correctness of the model 56.7 % 17 chains (278 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 21817 restraints for refining 11335 atoms. 17319 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2380 (Rfree = 0.000) for 11335 atoms. Found 101 (101 requested) and removed 79 (50 requested) atoms. Cycle 27: After refmac, R = 0.2235 (Rfree = 0.000) for 11306 atoms. Found 52 (101 requested) and removed 66 (50 requested) atoms. Cycle 28: After refmac, R = 0.2147 (Rfree = 0.000) for 11260 atoms. Found 36 (101 requested) and removed 56 (50 requested) atoms. Cycle 29: After refmac, R = 0.2124 (Rfree = 0.000) for 11228 atoms. Found 36 (100 requested) and removed 53 (50 requested) atoms. Cycle 30: After refmac, R = 0.2080 (Rfree = 0.000) for 11192 atoms. Found 26 (100 requested) and removed 51 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 11545 seeds are put forward NCS extension: 18 residues added (34 deleted due to clashes), 11563 seeds are put forward Round 1: 830 peptides, 108 chains. Longest chain 38 peptides. Score 0.521 Round 2: 923 peptides, 101 chains. Longest chain 50 peptides. Score 0.604 Round 3: 960 peptides, 101 chains. Longest chain 33 peptides. Score 0.627 Round 4: 931 peptides, 100 chains. Longest chain 34 peptides. Score 0.612 Round 5: 954 peptides, 110 chains. Longest chain 29 peptides. Score 0.598 Taking the results from Round 3 Chains 109, Residues 859, Estimated correctness of the model 48.1 % 15 chains (267 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22017 restraints for refining 11334 atoms. 17628 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2437 (Rfree = 0.000) for 11334 atoms. Found 54 (101 requested) and removed 102 (50 requested) atoms. Cycle 32: After refmac, R = 0.2195 (Rfree = 0.000) for 11233 atoms. Found 28 (101 requested) and removed 57 (50 requested) atoms. Cycle 33: After refmac, R = 0.2247 (Rfree = 0.000) for 11165 atoms. Found 95 (100 requested) and removed 70 (50 requested) atoms. Cycle 34: After refmac, R = 0.2316 (Rfree = 0.000) for 11155 atoms. Found 100 (100 requested) and removed 69 (50 requested) atoms. Cycle 35: After refmac, R = 0.2070 (Rfree = 0.000) for 11164 atoms. Found 69 (100 requested) and removed 63 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 11559 seeds are put forward NCS extension: 7 residues added (15 deleted due to clashes), 11566 seeds are put forward Round 1: 838 peptides, 118 chains. Longest chain 34 peptides. Score 0.494 Round 2: 922 peptides, 103 chains. Longest chain 30 peptides. Score 0.598 Round 3: 917 peptides, 90 chains. Longest chain 51 peptides. Score 0.632 Round 4: 890 peptides, 99 chains. Longest chain 34 peptides. Score 0.590 Round 5: 910 peptides, 99 chains. Longest chain 29 peptides. Score 0.602 Taking the results from Round 3 Chains 97, Residues 827, Estimated correctness of the model 49.4 % 13 chains (244 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22374 restraints for refining 11333 atoms. 18239 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2334 (Rfree = 0.000) for 11333 atoms. Found 82 (101 requested) and removed 67 (50 requested) atoms. Cycle 37: After refmac, R = 0.2443 (Rfree = 0.000) for 11303 atoms. Found 101 (101 requested) and removed 71 (50 requested) atoms. Cycle 38: After refmac, R = 0.2183 (Rfree = 0.000) for 11286 atoms. Found 85 (101 requested) and removed 69 (50 requested) atoms. Cycle 39: After refmac, R = 0.2609 (Rfree = 0.000) for 11274 atoms. Found 101 (101 requested) and removed 88 (50 requested) atoms. Cycle 40: After refmac, R = 0.2121 (Rfree = 0.000) for 11260 atoms. Found 70 (101 requested) and removed 66 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 11671 seeds are put forward NCS extension: 6 residues added (7 deleted due to clashes), 11677 seeds are put forward Round 1: 814 peptides, 116 chains. Longest chain 31 peptides. Score 0.483 Round 2: 905 peptides, 105 chains. Longest chain 35 peptides. Score 0.581 Round 3: 911 peptides, 101 chains. Longest chain 41 peptides. Score 0.597 Round 4: 941 peptides, 101 chains. Longest chain 43 peptides. Score 0.615 Round 5: 898 peptides, 105 chains. Longest chain 38 peptides. Score 0.577 Taking the results from Round 4 Chains 110, Residues 840, Estimated correctness of the model 45.0 % 17 chains (317 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 21774 restraints for refining 11333 atoms. 17287 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2451 (Rfree = 0.000) for 11333 atoms. Found 101 (101 requested) and removed 89 (50 requested) atoms. Cycle 42: After refmac, R = 0.2345 (Rfree = 0.000) for 11298 atoms. Found 92 (101 requested) and removed 69 (50 requested) atoms. Cycle 43: After refmac, R = 0.2389 (Rfree = 0.000) for 11283 atoms. Found 77 (101 requested) and removed 60 (50 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2133 (Rfree = 0.000) for 11251 atoms. Found 56 (101 requested) and removed 62 (50 requested) atoms. Cycle 45: After refmac, R = 0.2042 (Rfree = 0.000) for 11222 atoms. Found 52 (100 requested) and removed 61 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 11574 seeds are put forward NCS extension: 19 residues added (15 deleted due to clashes), 11593 seeds are put forward Round 1: 779 peptides, 117 chains. Longest chain 36 peptides. Score 0.453 Round 2: 879 peptides, 106 chains. Longest chain 34 peptides. Score 0.561 Round 3: 885 peptides, 111 chains. Longest chain 32 peptides. Score 0.550 Round 4: 887 peptides, 103 chains. Longest chain 51 peptides. Score 0.576 Round 5: 865 peptides, 112 chains. Longest chain 35 peptides. Score 0.533 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 111, Residues 784, Estimated correctness of the model 34.4 % 14 chains (246 residues) have been docked in sequence Sequence coverage is 31 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 169 B and 176 B 109 chains (789 residues) following loop building 13 chains (252 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 31643 reflections ( 99.89 % complete ) and 22593 restraints for refining 11335 atoms. 18577 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2574 (Rfree = 0.000) for 11335 atoms. Found 0 (101 requested) and removed 50 (50 requested) atoms. Cycle 47: After refmac, R = 0.2371 (Rfree = 0.000) for 11247 atoms. Found 0 (101 requested) and removed 50 (50 requested) atoms. Cycle 48: After refmac, R = 0.2778 (Rfree = 0.000) for 11162 atoms. Found 0 (100 requested) and removed 50 (50 requested) atoms. Cycle 49: After refmac, R = 0.2239 (Rfree = 0.000) for 11087 atoms. Found 0 (99 requested) and removed 49 (49 requested) atoms. Writing output files ... TimeTaking 131.93