null Sun 23 Dec 22:22:52 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 1vk2-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-3.2-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/1vk2-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-3.2-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 22:23:00 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/1vk2-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-3.2-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 161 and 0 Target number of residues in the AU: 161 Target solvent content: 0.6341 Checking the provided sequence file Detected sequence length: 204 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 204 Adjusted target solvent content: 0.54 Input MTZ file: 1vk2-3.2-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: 96 Cell parameters: 61.120 61.120 127.494 90.000 90.000 90.000 Input sequence file: 1vk2-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1632 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 55.114 3.200 Wilson plot Bfac: 67.56 4361 reflections ( 99.86 % complete ) and 0 restraints for refining 1796 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3422 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3084 (Rfree = 0.000) for 1796 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.03 Search for helices and strands: 0 residues in 0 chains, 1844 seeds are put forward Round 1: 99 peptides, 14 chains. Longest chain 17 peptides. Score 0.486 Round 2: 123 peptides, 17 chains. Longest chain 13 peptides. Score 0.548 Round 3: 137 peptides, 13 chains. Longest chain 30 peptides. Score 0.701 Round 4: 132 peptides, 12 chains. Longest chain 22 peptides. Score 0.700 Round 5: 137 peptides, 12 chains. Longest chain 31 peptides. Score 0.720 Taking the results from Round 5 Chains 12, Residues 125, Estimated correctness of the model 69.3 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 4361 reflections ( 99.86 % complete ) and 2900 restraints for refining 1489 atoms. 2311 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2651 (Rfree = 0.000) for 1489 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 2: After refmac, R = 0.2978 (Rfree = 0.000) for 1468 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 3: After refmac, R = 0.2468 (Rfree = 0.000) for 1441 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2320 (Rfree = 0.000) for 1423 atoms. Found 10 (11 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.2212 (Rfree = 0.000) for 1425 atoms. Found 4 (11 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 1484 seeds are put forward Round 1: 123 peptides, 13 chains. Longest chain 20 peptides. Score 0.641 Round 2: 144 peptides, 12 chains. Longest chain 24 peptides. Score 0.745 Round 3: 149 peptides, 13 chains. Longest chain 30 peptides. Score 0.745 Round 4: 150 peptides, 12 chains. Longest chain 27 peptides. Score 0.765 Round 5: 138 peptides, 13 chains. Longest chain 29 peptides. Score 0.705 Taking the results from Round 4 Chains 14, Residues 138, Estimated correctness of the model 77.7 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4361 reflections ( 99.86 % complete ) and 2993 restraints for refining 1485 atoms. 2379 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2730 (Rfree = 0.000) for 1485 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 7: After refmac, R = 0.2539 (Rfree = 0.000) for 1473 atoms. Found 9 (11 requested) and removed 12 (6 requested) atoms. Cycle 8: After refmac, R = 0.2698 (Rfree = 0.000) for 1467 atoms. Found 11 (11 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2267 (Rfree = 0.000) for 1459 atoms. Found 7 (11 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.2233 (Rfree = 0.000) for 1454 atoms. Found 5 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.04 Search for helices and strands: 0 residues in 0 chains, 1496 seeds are put forward Round 1: 141 peptides, 13 chains. Longest chain 35 peptides. Score 0.717 Round 2: 148 peptides, 12 chains. Longest chain 26 peptides. Score 0.758 Round 3: 148 peptides, 14 chains. Longest chain 27 peptides. Score 0.725 Round 4: 146 peptides, 13 chains. Longest chain 30 peptides. Score 0.735 Round 5: 151 peptides, 9 chains. Longest chain 36 peptides. Score 0.812 Taking the results from Round 5 Chains 9, Residues 142, Estimated correctness of the model 85.2 % 2 chains (47 residues) have been docked in sequence Building loops using Loopy2018 9 chains (142 residues) following loop building 2 chains (47 residues) in sequence following loop building ------------------------------------------------------ 4361 reflections ( 99.86 % complete ) and 2660 restraints for refining 1490 atoms. 1903 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2646 (Rfree = 0.000) for 1490 atoms. Found 10 (10 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.2365 (Rfree = 0.000) for 1473 atoms. Found 10 (10 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.2276 (Rfree = 0.000) for 1472 atoms. Found 4 (10 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.2291 (Rfree = 0.000) for 1466 atoms. Found 3 (10 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.2248 (Rfree = 0.000) for 1457 atoms. Found 7 (9 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 1506 seeds are put forward Round 1: 134 peptides, 13 chains. Longest chain 18 peptides. Score 0.689 Round 2: 143 peptides, 11 chains. Longest chain 28 peptides. Score 0.758 Round 3: 134 peptides, 11 chains. Longest chain 39 peptides. Score 0.727 Round 4: 135 peptides, 15 chains. Longest chain 20 peptides. Score 0.653 Round 5: 141 peptides, 14 chains. Longest chain 22 peptides. Score 0.698 Taking the results from Round 2 Chains 11, Residues 132, Estimated correctness of the model 76.5 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4361 reflections ( 99.86 % complete ) and 2992 restraints for refining 1490 atoms. 2388 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2424 (Rfree = 0.000) for 1490 atoms. Found 9 (9 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2326 (Rfree = 0.000) for 1484 atoms. Found 9 (9 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2283 (Rfree = 0.000) for 1484 atoms. Found 6 (9 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2303 (Rfree = 0.000) for 1483 atoms. Found 4 (8 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2219 (Rfree = 0.000) for 1481 atoms. Found 1 (8 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 1533 seeds are put forward Round 1: 120 peptides, 14 chains. Longest chain 23 peptides. Score 0.604 Round 2: 130 peptides, 11 chains. Longest chain 51 peptides. Score 0.711 Round 3: 136 peptides, 11 chains. Longest chain 31 peptides. Score 0.734 Round 4: 134 peptides, 14 chains. Longest chain 19 peptides. Score 0.669 Round 5: 137 peptides, 14 chains. Longest chain 30 peptides. Score 0.682 Taking the results from Round 3 Chains 11, Residues 125, Estimated correctness of the model 72.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4361 reflections ( 99.86 % complete ) and 3257 restraints for refining 1490 atoms. 2768 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2472 (Rfree = 0.000) for 1490 atoms. Found 8 (8 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2842 (Rfree = 0.000) for 1487 atoms. Found 8 (8 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2217 (Rfree = 0.000) for 1484 atoms. Found 3 (7 requested) and removed 9 (6 requested) atoms. Cycle 24: After refmac, R = 0.2811 (Rfree = 0.000) for 1474 atoms. Found 7 (7 requested) and removed 16 (6 requested) atoms. Cycle 25: After refmac, R = 0.2221 (Rfree = 0.000) for 1464 atoms. Found 7 (7 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.03 Search for helices and strands: 0 residues in 0 chains, 1521 seeds are put forward Round 1: 134 peptides, 14 chains. Longest chain 33 peptides. Score 0.669 Round 2: 138 peptides, 15 chains. Longest chain 19 peptides. Score 0.666 Round 3: 140 peptides, 12 chains. Longest chain 30 peptides. Score 0.731 Round 4: 148 peptides, 14 chains. Longest chain 25 peptides. Score 0.725 Round 5: 146 peptides, 12 chains. Longest chain 28 peptides. Score 0.752 Taking the results from Round 5 Chains 13, Residues 134, Estimated correctness of the model 75.4 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4361 reflections ( 99.86 % complete ) and 2871 restraints for refining 1490 atoms. 2256 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2465 (Rfree = 0.000) for 1490 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. Cycle 27: After refmac, R = 0.2277 (Rfree = 0.000) for 1486 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.2380 (Rfree = 0.000) for 1480 atoms. Found 6 (6 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.2114 (Rfree = 0.000) for 1479 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.2046 (Rfree = 0.000) for 1475 atoms. Found 6 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 1530 seeds are put forward Round 1: 132 peptides, 16 chains. Longest chain 13 peptides. Score 0.618 Round 2: 140 peptides, 15 chains. Longest chain 22 peptides. Score 0.675 Round 3: 148 peptides, 15 chains. Longest chain 25 peptides. Score 0.707 Round 4: 147 peptides, 18 chains. Longest chain 19 peptides. Score 0.646 Round 5: 147 peptides, 15 chains. Longest chain 25 peptides. Score 0.703 Taking the results from Round 3 Chains 15, Residues 133, Estimated correctness of the model 66.7 % 2 chains (21 residues) have been docked in sequence Building loops using Loopy2018 15 chains (133 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ 4361 reflections ( 99.86 % complete ) and 3055 restraints for refining 1489 atoms. 2471 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2388 (Rfree = 0.000) for 1489 atoms. Found 6 (6 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2230 (Rfree = 0.000) for 1477 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.2181 (Rfree = 0.000) for 1472 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. Cycle 34: After refmac, R = 0.2170 (Rfree = 0.000) for 1467 atoms. Found 5 (6 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2094 (Rfree = 0.000) for 1465 atoms. Found 4 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 1516 seeds are put forward Round 1: 120 peptides, 15 chains. Longest chain 14 peptides. Score 0.580 Round 2: 132 peptides, 15 chains. Longest chain 21 peptides. Score 0.639 Round 3: 132 peptides, 15 chains. Longest chain 19 peptides. Score 0.639 Round 4: 137 peptides, 15 chains. Longest chain 21 peptides. Score 0.662 Round 5: 140 peptides, 15 chains. Longest chain 25 peptides. Score 0.675 Taking the results from Round 5 Chains 15, Residues 125, Estimated correctness of the model 59.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4361 reflections ( 99.86 % complete ) and 3144 restraints for refining 1490 atoms. 2632 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2476 (Rfree = 0.000) for 1490 atoms. Found 6 (6 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.2364 (Rfree = 0.000) for 1487 atoms. Found 6 (6 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.2341 (Rfree = 0.000) for 1484 atoms. Found 6 (6 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2307 (Rfree = 0.000) for 1483 atoms. Found 3 (6 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.2210 (Rfree = 0.000) for 1475 atoms. Found 6 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.03 Search for helices and strands: 0 residues in 0 chains, 1529 seeds are put forward Round 1: 130 peptides, 17 chains. Longest chain 23 peptides. Score 0.585 Round 2: 136 peptides, 15 chains. Longest chain 24 peptides. Score 0.658 Round 3: 134 peptides, 15 chains. Longest chain 25 peptides. Score 0.649 Round 4: 126 peptides, 14 chains. Longest chain 20 peptides. Score 0.633 Round 5: 129 peptides, 14 chains. Longest chain 23 peptides. Score 0.647 Taking the results from Round 2 Chains 15, Residues 121, Estimated correctness of the model 55.7 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4361 reflections ( 99.86 % complete ) and 3181 restraints for refining 1490 atoms. 2685 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2308 (Rfree = 0.000) for 1490 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.2229 (Rfree = 0.000) for 1486 atoms. Found 6 (6 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2191 (Rfree = 0.000) for 1485 atoms. Found 5 (6 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2219 (Rfree = 0.000) for 1484 atoms. Found 3 (6 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2184 (Rfree = 0.000) for 1480 atoms. Found 3 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.04 Search for helices and strands: 0 residues in 0 chains, 1526 seeds are put forward Round 1: 122 peptides, 15 chains. Longest chain 22 peptides. Score 0.591 Round 2: 122 peptides, 15 chains. Longest chain 22 peptides. Score 0.591 Round 3: 123 peptides, 15 chains. Longest chain 23 peptides. Score 0.596 Round 4: 124 peptides, 17 chains. Longest chain 14 peptides. Score 0.554 Round 5: 129 peptides, 15 chains. Longest chain 18 peptides. Score 0.625 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 114, Estimated correctness of the model 47.6 % 2 chains (24 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 1vk2-3_warpNtrace.pdb as input Building loops using Loopy2018 15 chains (114 residues) following loop building 2 chains (24 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4361 reflections ( 99.86 % complete ) and 3121 restraints for refining 1490 atoms. 2601 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2448 (Rfree = 0.000) for 1490 atoms. Found 0 (6 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2326 (Rfree = 0.000) for 1483 atoms. Found 0 (6 requested) and removed 4 (6 requested) atoms. Cycle 48: After refmac, R = 0.2254 (Rfree = 0.000) for 1479 atoms. Found 0 (6 requested) and removed 2 (6 requested) atoms. Cycle 49: After refmac, R = 0.2231 (Rfree = 0.000) for 1477 atoms. Found 0 (6 requested) and removed 5 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:55 GMT 2018 Job finished. TimeTaking 31.04 Used memory is bytes: 16760592