null Sun 23 Dec 22:22:59 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 2hdo-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-4.0-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/2hdo-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-4.0-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 22:23:08 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/2hdo-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-4.0-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 126 and 0 Target number of residues in the AU: 126 Target solvent content: 0.6703 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 209 Adjusted target solvent content: 0.45 Input MTZ file: 2hdo-4.0-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: 169 Cell parameters: 87.040 87.040 47.290 90.000 90.000 120.000 Input sequence file: 2hdo-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1672 target number of atoms Had to go as low as 0.80 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: 29.474 4.003 Wilson plot Bfac: 91.16 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1789 reflections ( 99.44 % complete ) and 0 restraints for refining 1859 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3457 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2517 (Rfree = 0.000) for 1859 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 4.01 Search for helices and strands: 0 residues in 0 chains, 1893 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 14 peptides. Score 0.307 Round 2: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.351 Round 3: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.332 Round 4: 101 peptides, 15 chains. Longest chain 17 peptides. Score 0.503 Round 5: 99 peptides, 13 chains. Longest chain 17 peptides. Score 0.548 Taking the results from Round 5 Chains 14, Residues 86, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1789 reflections ( 99.44 % complete ) and 3662 restraints for refining 1510 atoms. 3304 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.1960 (Rfree = 0.000) for 1510 atoms. Found 3 (7 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.1865 (Rfree = 0.000) for 1490 atoms. Found 0 (7 requested) and removed 11 (3 requested) atoms. Cycle 3: After refmac, R = 0.1747 (Rfree = 0.000) for 1475 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2076 (Rfree = 0.000) for 1467 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2288 (Rfree = 0.000) for 1461 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.88 4.15 Search for helices and strands: 0 residues in 0 chains, 1541 seeds are put forward Round 1: 92 peptides, 16 chains. Longest chain 13 peptides. Score 0.407 Round 2: 102 peptides, 16 chains. Longest chain 13 peptides. Score 0.480 Round 3: 108 peptides, 17 chains. Longest chain 13 peptides. Score 0.491 Round 4: 105 peptides, 17 chains. Longest chain 9 peptides. Score 0.470 Round 5: 115 peptides, 15 chains. Longest chain 20 peptides. Score 0.591 Taking the results from Round 5 Chains 16, Residues 100, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 1789 reflections ( 99.44 % complete ) and 3318 restraints for refining 1510 atoms. 2880 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1985 (Rfree = 0.000) for 1510 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 7: After refmac, R = 0.1958 (Rfree = 0.000) for 1476 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 8: After refmac, R = 0.1926 (Rfree = 0.000) for 1460 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.1691 (Rfree = 0.000) for 1453 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1549 (Rfree = 0.000) for 1448 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.85 4.12 Search for helices and strands: 0 residues in 0 chains, 1507 seeds are put forward Round 1: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.389 Round 2: 110 peptides, 17 chains. Longest chain 15 peptides. Score 0.505 Round 3: 99 peptides, 14 chains. Longest chain 15 peptides. Score 0.519 Round 4: 119 peptides, 19 chains. Longest chain 12 peptides. Score 0.507 Round 5: 107 peptides, 14 chains. Longest chain 15 peptides. Score 0.570 Taking the results from Round 5 Chains 14, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1789 reflections ( 99.44 % complete ) and 3546 restraints for refining 1499 atoms. 3188 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1901 (Rfree = 0.000) for 1499 atoms. Found 3 (7 requested) and removed 29 (3 requested) atoms. Cycle 12: After refmac, R = 0.1780 (Rfree = 0.000) for 1454 atoms. Found 2 (6 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.1605 (Rfree = 0.000) for 1442 atoms. Found 0 (6 requested) and removed 13 (3 requested) atoms. Cycle 14: After refmac, R = 0.1760 (Rfree = 0.000) for 1427 atoms. Found 2 (6 requested) and removed 8 (3 requested) atoms. Cycle 15: After refmac, R = 0.1596 (Rfree = 0.000) for 1418 atoms. Found 0 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.86 4.13 Search for helices and strands: 0 residues in 0 chains, 1473 seeds are put forward Round 1: 71 peptides, 17 chains. Longest chain 6 peptides. Score 0.195 Round 2: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.276 Round 3: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.335 Round 4: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.367 Round 5: 84 peptides, 14 chains. Longest chain 10 peptides. Score 0.411 Taking the results from Round 5 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1789 reflections ( 99.44 % complete ) and 3543 restraints for refining 1473 atoms. 3277 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1791 (Rfree = 0.000) for 1473 atoms. Found 1 (6 requested) and removed 61 (3 requested) atoms. Cycle 17: After refmac, R = 0.1758 (Rfree = 0.000) for 1409 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 18: After refmac, R = 0.1599 (Rfree = 0.000) for 1402 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.1665 (Rfree = 0.000) for 1393 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.1493 (Rfree = 0.000) for 1390 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.89 4.16 Search for helices and strands: 0 residues in 0 chains, 1441 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 11 peptides. Score 0.299 Round 2: 93 peptides, 19 chains. Longest chain 7 peptides. Score 0.314 Round 3: 89 peptides, 16 chains. Longest chain 11 peptides. Score 0.383 Round 4: 87 peptides, 15 chains. Longest chain 9 peptides. Score 0.401 Round 5: 86 peptides, 16 chains. Longest chain 8 peptides. Score 0.359 Taking the results from Round 4 Chains 15, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1789 reflections ( 99.44 % complete ) and 3676 restraints for refining 1510 atoms. 3403 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1968 (Rfree = 0.000) for 1510 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 22: After refmac, R = 0.1612 (Rfree = 0.000) for 1496 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.1632 (Rfree = 0.000) for 1491 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.1531 (Rfree = 0.000) for 1483 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.1710 (Rfree = 0.000) for 1479 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 4.11 Search for helices and strands: 0 residues in 0 chains, 1526 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.303 Round 2: 80 peptides, 13 chains. Longest chain 10 peptides. Score 0.414 Round 3: 79 peptides, 12 chains. Longest chain 17 peptides. Score 0.440 Round 4: 85 peptides, 14 chains. Longest chain 9 peptides. Score 0.419 Round 5: 84 peptides, 13 chains. Longest chain 9 peptides. Score 0.444 Taking the results from Round 5 Chains 13, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1789 reflections ( 99.44 % complete ) and 3566 restraints for refining 1510 atoms. 3295 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1943 (Rfree = 0.000) for 1510 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 27: After refmac, R = 0.1788 (Rfree = 0.000) for 1507 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.1641 (Rfree = 0.000) for 1505 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.1659 (Rfree = 0.000) for 1499 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.1667 (Rfree = 0.000) for 1494 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.86 4.13 Search for helices and strands: 0 residues in 0 chains, 1535 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.312 Round 2: 66 peptides, 12 chains. Longest chain 9 peptides. Score 0.336 Round 3: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.374 Round 4: 74 peptides, 12 chains. Longest chain 10 peptides. Score 0.401 Round 5: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 4 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1789 reflections ( 99.44 % complete ) and 3751 restraints for refining 1510 atoms. 3515 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2017 (Rfree = 0.000) for 1510 atoms. Found 6 (7 requested) and removed 11 (3 requested) atoms. Cycle 32: After refmac, R = 0.1626 (Rfree = 0.000) for 1504 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.1613 (Rfree = 0.000) for 1496 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.1503 (Rfree = 0.000) for 1489 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1449 (Rfree = 0.000) for 1485 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.85 4.12 Search for helices and strands: 0 residues in 0 chains, 1529 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 6 peptides. Score 0.272 Round 2: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.356 Round 3: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.364 Round 4: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.356 Round 5: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 5 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1789 reflections ( 99.44 % complete ) and 3465 restraints for refining 1474 atoms. 3236 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1851 (Rfree = 0.000) for 1474 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 37: After refmac, R = 0.1727 (Rfree = 0.000) for 1465 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.1603 (Rfree = 0.000) for 1466 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.1494 (Rfree = 0.000) for 1467 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1473 (Rfree = 0.000) for 1463 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 4.12 Search for helices and strands: 0 residues in 0 chains, 1512 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 7 peptides. Score 0.228 Round 2: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.274 Round 3: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.385 Round 4: 77 peptides, 13 chains. Longest chain 11 peptides. Score 0.391 Round 5: 77 peptides, 12 chains. Longest chain 12 peptides. Score 0.425 Taking the results from Round 5 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1789 reflections ( 99.44 % complete ) and 3616 restraints for refining 1501 atoms. 3368 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1609 (Rfree = 0.000) for 1501 atoms. Found 2 (7 requested) and removed 9 (3 requested) atoms. Cycle 42: After refmac, R = 0.1657 (Rfree = 0.000) for 1488 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.1343 (Rfree = 0.000) for 1486 atoms. Found 0 (7 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.1302 (Rfree = 0.000) for 1477 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.1798 (Rfree = 0.000) for 1471 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 4.09 Search for helices and strands: 0 residues in 0 chains, 1511 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 6 peptides. Score 0.197 Round 2: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.312 Round 3: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.283 Round 4: 60 peptides, 11 chains. Longest chain 9 peptides. Score 0.321 Round 5: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.339 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hdo-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1789 reflections ( 99.44 % complete ) and 3561 restraints for refining 1476 atoms. 3368 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1595 (Rfree = 0.000) for 1476 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1484 (Rfree = 0.000) for 1469 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1431 (Rfree = 0.000) for 1463 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1782 (Rfree = 0.000) for 1458 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:10 GMT 2018 Job finished. TimeTaking 29.19 Used memory is bytes: 20539608