null Sun 23 Dec 22:22:40 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 2gm6-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.6-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/2gm6-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.6-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 ============================================================ Sun 23 Dec 22:22:49 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/2gm6-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.6-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 226 and 0 Target number of residues in the AU: 226 Target solvent content: 0.6525 Checking the provided sequence file Detected sequence length: 208 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 208 Adjusted target solvent content: 0.68 Input MTZ file: 2gm6-3.6-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: 92 Cell parameters: 57.001 57.001 216.648 90.000 90.000 90.000 Input sequence file: 2gm6-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1664 target number of atoms Had to go as low as 1.00 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: 55.125 3.601 Wilson plot Bfac: 79.05 4596 reflections ( 99.72 % complete ) and 0 restraints for refining 1864 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3674 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3130 (Rfree = 0.000) for 1864 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 2.70 Search for helices and strands: 0 residues in 0 chains, 1894 seeds are put forward Round 1: 133 peptides, 17 chains. Longest chain 17 peptides. Score 0.500 Round 2: 152 peptides, 17 chains. Longest chain 24 peptides. Score 0.574 Round 3: 149 peptides, 15 chains. Longest chain 30 peptides. Score 0.597 Round 4: 148 peptides, 14 chains. Longest chain 22 peptides. Score 0.610 Round 5: 157 peptides, 14 chains. Longest chain 26 peptides. Score 0.640 Taking the results from Round 5 Chains 19, Residues 143, Estimated correctness of the model 29.6 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 4596 reflections ( 99.72 % complete ) and 3026 restraints for refining 1553 atoms. 2344 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2845 (Rfree = 0.000) for 1553 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 2: After refmac, R = 0.2585 (Rfree = 0.000) for 1518 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 3: After refmac, R = 0.2457 (Rfree = 0.000) for 1506 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2459 (Rfree = 0.000) for 1491 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2337 (Rfree = 0.000) for 1486 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 2.68 Search for helices and strands: 0 residues in 0 chains, 1536 seeds are put forward Round 1: 150 peptides, 17 chains. Longest chain 28 peptides. Score 0.567 Round 2: 151 peptides, 14 chains. Longest chain 40 peptides. Score 0.620 Round 3: 162 peptides, 17 chains. Longest chain 29 peptides. Score 0.609 Round 4: 154 peptides, 15 chains. Longest chain 31 peptides. Score 0.614 Round 5: 148 peptides, 14 chains. Longest chain 28 peptides. Score 0.610 Taking the results from Round 2 Chains 20, Residues 137, Estimated correctness of the model 22.2 % 5 chains (50 residues) have been docked in sequence ------------------------------------------------------ 4596 reflections ( 99.72 % complete ) and 2780 restraints for refining 1509 atoms. 2079 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2605 (Rfree = 0.000) for 1509 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 7: After refmac, R = 0.2435 (Rfree = 0.000) for 1486 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 8: After refmac, R = 0.2411 (Rfree = 0.000) for 1468 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.2312 (Rfree = 0.000) for 1466 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.2254 (Rfree = 0.000) for 1460 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 2.72 Search for helices and strands: 0 residues in 0 chains, 1507 seeds are put forward Round 1: 146 peptides, 14 chains. Longest chain 27 peptides. Score 0.603 Round 2: 151 peptides, 16 chains. Longest chain 38 peptides. Score 0.587 Round 3: 154 peptides, 15 chains. Longest chain 24 peptides. Score 0.614 Round 4: 158 peptides, 16 chains. Longest chain 25 peptides. Score 0.612 Round 5: 157 peptides, 14 chains. Longest chain 24 peptides. Score 0.640 Taking the results from Round 5 Chains 16, Residues 143, Estimated correctness of the model 29.6 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 4596 reflections ( 99.72 % complete ) and 2847 restraints for refining 1509 atoms. 2156 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2659 (Rfree = 0.000) for 1509 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 12: After refmac, R = 0.2474 (Rfree = 0.000) for 1500 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 13: After refmac, R = 0.2421 (Rfree = 0.000) for 1486 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.2568 (Rfree = 0.000) for 1486 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.2471 (Rfree = 0.000) for 1480 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 2.72 Search for helices and strands: 0 residues in 0 chains, 1536 seeds are put forward Round 1: 150 peptides, 15 chains. Longest chain 26 peptides. Score 0.601 Round 2: 157 peptides, 13 chains. Longest chain 32 peptides. Score 0.656 Round 3: 156 peptides, 13 chains. Longest chain 28 peptides. Score 0.653 Round 4: 155 peptides, 9 chains. Longest chain 44 peptides. Score 0.709 Round 5: 157 peptides, 13 chains. Longest chain 40 peptides. Score 0.656 Taking the results from Round 4 Chains 12, Residues 146, Estimated correctness of the model 52.3 % 2 chains (37 residues) have been docked in sequence Building loops using Loopy2018 12 chains (146 residues) following loop building 2 chains (37 residues) in sequence following loop building ------------------------------------------------------ 4596 reflections ( 99.72 % complete ) and 2761 restraints for refining 1509 atoms. 2012 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2574 (Rfree = 0.000) for 1509 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 17: After refmac, R = 0.2379 (Rfree = 0.000) for 1495 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.2291 (Rfree = 0.000) for 1489 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2245 (Rfree = 0.000) for 1491 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2360 (Rfree = 0.000) for 1488 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 2.68 Search for helices and strands: 0 residues in 0 chains, 1551 seeds are put forward Round 1: 154 peptides, 14 chains. Longest chain 32 peptides. Score 0.630 Round 2: 155 peptides, 13 chains. Longest chain 42 peptides. Score 0.649 Round 3: 148 peptides, 14 chains. Longest chain 37 peptides. Score 0.610 Round 4: 150 peptides, 13 chains. Longest chain 28 peptides. Score 0.633 Round 5: 149 peptides, 12 chains. Longest chain 37 peptides. Score 0.646 Taking the results from Round 2 Chains 16, Residues 142, Estimated correctness of the model 32.7 % 3 chains (50 residues) have been docked in sequence ------------------------------------------------------ 4596 reflections ( 99.72 % complete ) and 2810 restraints for refining 1509 atoms. 2044 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2705 (Rfree = 0.000) for 1509 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 22: After refmac, R = 0.2632 (Rfree = 0.000) for 1499 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 23: After refmac, R = 0.2853 (Rfree = 0.000) for 1494 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 24: After refmac, R = 0.2709 (Rfree = 0.000) for 1483 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 25: After refmac, R = 0.2686 (Rfree = 0.000) for 1477 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 2.69 Search for helices and strands: 0 residues in 0 chains, 1528 seeds are put forward Round 1: 142 peptides, 16 chains. Longest chain 20 peptides. Score 0.554 Round 2: 157 peptides, 12 chains. Longest chain 31 peptides. Score 0.671 Round 3: 144 peptides, 10 chains. Longest chain 38 peptides. Score 0.662 Round 4: 145 peptides, 15 chains. Longest chain 21 peptides. Score 0.583 Round 5: 151 peptides, 13 chains. Longest chain 25 peptides. Score 0.637 Taking the results from Round 2 Chains 14, Residues 145, Estimated correctness of the model 40.3 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 4596 reflections ( 99.72 % complete ) and 2756 restraints for refining 1509 atoms. 2016 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2711 (Rfree = 0.000) for 1509 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 27: After refmac, R = 0.2608 (Rfree = 0.000) for 1484 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.2263 (Rfree = 0.000) for 1477 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.2200 (Rfree = 0.000) for 1475 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.2138 (Rfree = 0.000) for 1474 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 2.71 Search for helices and strands: 0 residues in 0 chains, 1523 seeds are put forward Round 1: 145 peptides, 15 chains. Longest chain 21 peptides. Score 0.583 Round 2: 150 peptides, 11 chains. Longest chain 36 peptides. Score 0.665 Round 3: 164 peptides, 12 chains. Longest chain 38 peptides. Score 0.692 Round 4: 148 peptides, 11 chains. Longest chain 30 peptides. Score 0.659 Round 5: 138 peptides, 13 chains. Longest chain 23 peptides. Score 0.592 Taking the results from Round 3 Chains 13, Residues 152, Estimated correctness of the model 47.1 % 2 chains (56 residues) have been docked in sequence ------------------------------------------------------ 4596 reflections ( 99.72 % complete ) and 2524 restraints for refining 1509 atoms. 1663 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2672 (Rfree = 0.000) for 1509 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 32: After refmac, R = 0.2732 (Rfree = 0.000) for 1495 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 33: After refmac, R = 0.2383 (Rfree = 0.000) for 1482 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 34: After refmac, R = 0.2226 (Rfree = 0.000) for 1469 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2154 (Rfree = 0.000) for 1471 atoms. Found 5 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 2.70 Search for helices and strands: 0 residues in 0 chains, 1512 seeds are put forward Round 1: 142 peptides, 16 chains. Longest chain 23 peptides. Score 0.554 Round 2: 140 peptides, 11 chains. Longest chain 26 peptides. Score 0.633 Round 3: 147 peptides, 17 chains. Longest chain 24 peptides. Score 0.555 Round 4: 152 peptides, 14 chains. Longest chain 26 peptides. Score 0.624 Round 5: 156 peptides, 14 chains. Longest chain 31 peptides. Score 0.637 Taking the results from Round 5 Chains 14, Residues 142, Estimated correctness of the model 28.5 % 2 chains (53 residues) have been docked in sequence ------------------------------------------------------ 4596 reflections ( 99.72 % complete ) and 2705 restraints for refining 1509 atoms. 1900 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2680 (Rfree = 0.000) for 1509 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 37: After refmac, R = 0.2506 (Rfree = 0.000) for 1501 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.2430 (Rfree = 0.000) for 1501 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 39: After refmac, R = 0.2365 (Rfree = 0.000) for 1498 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.2302 (Rfree = 0.000) for 1497 atoms. Found 4 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 2.70 Search for helices and strands: 0 residues in 0 chains, 1540 seeds are put forward Round 1: 139 peptides, 16 chains. Longest chain 21 peptides. Score 0.543 Round 2: 146 peptides, 14 chains. Longest chain 35 peptides. Score 0.603 Round 3: 148 peptides, 15 chains. Longest chain 25 peptides. Score 0.594 Round 4: 150 peptides, 17 chains. Longest chain 25 peptides. Score 0.567 Round 5: 139 peptides, 13 chains. Longest chain 25 peptides. Score 0.596 Taking the results from Round 2 Chains 14, Residues 132, Estimated correctness of the model 15.7 % 3 chains (55 residues) have been docked in sequence ------------------------------------------------------ 4596 reflections ( 99.72 % complete ) and 2752 restraints for refining 1509 atoms. 1985 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2484 (Rfree = 0.000) for 1509 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 42: After refmac, R = 0.2270 (Rfree = 0.000) for 1492 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.2126 (Rfree = 0.000) for 1489 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.2031 (Rfree = 0.000) for 1477 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1977 (Rfree = 0.000) for 1476 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 2.69 Search for helices and strands: 0 residues in 0 chains, 1509 seeds are put forward Round 1: 138 peptides, 15 chains. Longest chain 21 peptides. Score 0.557 Round 2: 141 peptides, 15 chains. Longest chain 38 peptides. Score 0.568 Round 3: 142 peptides, 15 chains. Longest chain 19 peptides. Score 0.572 Round 4: 149 peptides, 13 chains. Longest chain 38 peptides. Score 0.630 Round 5: 147 peptides, 10 chains. Longest chain 39 peptides. Score 0.671 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 137, Estimated correctness of the model 40.3 % 2 chains (38 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 2gm6-3_warpNtrace.pdb as input Building loops using Loopy2018 12 chains (137 residues) following loop building 2 chains (38 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4596 reflections ( 99.72 % complete ) and 2848 restraints for refining 1508 atoms. 2150 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2487 (Rfree = 0.000) for 1508 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2350 (Rfree = 0.000) for 1492 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2265 (Rfree = 0.000) for 1476 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2223 (Rfree = 0.000) for 1471 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:58 GMT 2018 Job finished. TimeTaking 34.3 Used memory is bytes: 3870680