Sun 23 Dec 22:22:44 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 2o2x-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-3.4-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/2o2x-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-3.4-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 22:22:52 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/2o2x-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-3.4-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 130 and 0 Target number of residues in the AU: 130 Target solvent content: 0.6255 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 218 Adjusted target solvent content: 0.37 Input MTZ file: 2o2x-3.4-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: 4 Cell parameters: 36.470 66.250 41.010 90.000 108.540 90.000 Input sequence file: 2o2x-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1744 target number of atoms Had to go as low as 0.65 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: 38.882 3.400 Wilson plot Bfac: 62.99 2576 reflections ( 99.27 % complete ) and 0 restraints for refining 1938 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3044 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2573 (Rfree = 0.000) for 1938 atoms. Found 12 (14 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.84 Search for helices and strands: 0 residues in 0 chains, 1980 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 8 peptides. Score 0.264 Round 2: 103 peptides, 18 chains. Longest chain 13 peptides. Score 0.444 Round 3: 107 peptides, 16 chains. Longest chain 16 peptides. Score 0.537 Round 4: 119 peptides, 17 chains. Longest chain 13 peptides. Score 0.588 Round 5: 116 peptides, 18 chains. Longest chain 18 peptides. Score 0.539 Taking the results from Round 4 Chains 17, Residues 102, Estimated correctness of the model 24.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2576 reflections ( 99.27 % complete ) and 3462 restraints for refining 1584 atoms. 3037 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2011 (Rfree = 0.000) for 1584 atoms. Found 10 (11 requested) and removed 11 (5 requested) atoms. Cycle 2: After refmac, R = 0.1849 (Rfree = 0.000) for 1559 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.1569 (Rfree = 0.000) for 1545 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 4: After refmac, R = 0.1628 (Rfree = 0.000) for 1537 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.1482 (Rfree = 0.000) for 1531 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 3.83 Search for helices and strands: 0 residues in 0 chains, 1580 seeds are put forward Round 1: 95 peptides, 18 chains. Longest chain 12 peptides. Score 0.378 Round 2: 120 peptides, 20 chains. Longest chain 13 peptides. Score 0.507 Round 3: 113 peptides, 18 chains. Longest chain 13 peptides. Score 0.518 Round 4: 115 peptides, 17 chains. Longest chain 13 peptides. Score 0.562 Round 5: 103 peptides, 16 chains. Longest chain 12 peptides. Score 0.509 Taking the results from Round 4 Chains 17, Residues 98, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2576 reflections ( 99.27 % complete ) and 3568 restraints for refining 1555 atoms. 3193 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1763 (Rfree = 0.000) for 1555 atoms. Found 1 (11 requested) and removed 10 (5 requested) atoms. Cycle 7: After refmac, R = 0.1566 (Rfree = 0.000) for 1539 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 8: After refmac, R = 0.1462 (Rfree = 0.000) for 1534 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.1386 (Rfree = 0.000) for 1532 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.1652 (Rfree = 0.000) for 1527 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.80 Search for helices and strands: 0 residues in 0 chains, 1568 seeds are put forward Round 1: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.426 Round 2: 107 peptides, 18 chains. Longest chain 12 peptides. Score 0.474 Round 3: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.467 Round 4: 97 peptides, 15 chains. Longest chain 12 peptides. Score 0.496 Round 5: 104 peptides, 15 chains. Longest chain 13 peptides. Score 0.547 Taking the results from Round 5 Chains 15, Residues 89, Estimated correctness of the model 10.4 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2576 reflections ( 99.27 % complete ) and 3615 restraints for refining 1579 atoms. 3258 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1740 (Rfree = 0.000) for 1579 atoms. Found 2 (11 requested) and removed 12 (5 requested) atoms. Cycle 12: After refmac, R = 0.1734 (Rfree = 0.000) for 1561 atoms. Found 0 (11 requested) and removed 11 (5 requested) atoms. Cycle 13: After refmac, R = 0.1981 (Rfree = 0.000) for 1548 atoms. Found 7 (11 requested) and removed 11 (5 requested) atoms. Cycle 14: After refmac, R = 0.1684 (Rfree = 0.000) for 1543 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.1724 (Rfree = 0.000) for 1538 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.78 Search for helices and strands: 0 residues in 0 chains, 1593 seeds are put forward Round 1: 99 peptides, 19 chains. Longest chain 8 peptides. Score 0.377 Round 2: 103 peptides, 16 chains. Longest chain 16 peptides. Score 0.509 Round 3: 104 peptides, 18 chains. Longest chain 14 peptides. Score 0.451 Round 4: 108 peptides, 16 chains. Longest chain 17 peptides. Score 0.544 Round 5: 98 peptides, 15 chains. Longest chain 14 peptides. Score 0.504 Taking the results from Round 4 Chains 16, Residues 92, Estimated correctness of the model 9.3 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2576 reflections ( 99.27 % complete ) and 3662 restraints for refining 1585 atoms. 3294 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1613 (Rfree = 0.000) for 1585 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 17: After refmac, R = 0.1471 (Rfree = 0.000) for 1573 atoms. Found 0 (11 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.1339 (Rfree = 0.000) for 1562 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.1457 (Rfree = 0.000) for 1551 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1452 (Rfree = 0.000) for 1550 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.83 Search for helices and strands: 0 residues in 0 chains, 1609 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.325 Round 2: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.416 Round 3: 93 peptides, 15 chains. Longest chain 19 peptides. Score 0.466 Round 4: 92 peptides, 14 chains. Longest chain 14 peptides. Score 0.492 Round 5: 79 peptides, 11 chains. Longest chain 12 peptides. Score 0.494 Taking the results from Round 5 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2576 reflections ( 99.27 % complete ) and 3761 restraints for refining 1585 atoms. 3500 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1556 (Rfree = 0.000) for 1585 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 22: After refmac, R = 0.1550 (Rfree = 0.000) for 1578 atoms. Found 5 (11 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.1525 (Rfree = 0.000) for 1572 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.1393 (Rfree = 0.000) for 1571 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.1623 (Rfree = 0.000) for 1568 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.84 Search for helices and strands: 0 residues in 0 chains, 1632 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.306 Round 2: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.448 Round 3: 73 peptides, 13 chains. Longest chain 12 peptides. Score 0.372 Round 4: 87 peptides, 12 chains. Longest chain 16 peptides. Score 0.520 Round 5: 93 peptides, 13 chains. Longest chain 14 peptides. Score 0.531 Taking the results from Round 5 Chains 13, Residues 80, Estimated correctness of the model 4.6 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2576 reflections ( 99.27 % complete ) and 3639 restraints for refining 1585 atoms. 3312 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1562 (Rfree = 0.000) for 1585 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. Cycle 27: After refmac, R = 0.1395 (Rfree = 0.000) for 1576 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1445 (Rfree = 0.000) for 1572 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1378 (Rfree = 0.000) for 1569 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1452 (Rfree = 0.000) for 1566 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.89 Search for helices and strands: 0 residues in 0 chains, 1605 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 7 peptides. Score 0.225 Round 2: 73 peptides, 14 chains. Longest chain 12 peptides. Score 0.333 Round 3: 78 peptides, 16 chains. Longest chain 13 peptides. Score 0.302 Round 4: 83 peptides, 16 chains. Longest chain 12 peptides. Score 0.347 Round 5: 76 peptides, 14 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 5 Chains 14, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2576 reflections ( 99.27 % complete ) and 3837 restraints for refining 1585 atoms. 3603 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1524 (Rfree = 0.000) for 1585 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 32: After refmac, R = 0.1313 (Rfree = 0.000) for 1587 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.1275 (Rfree = 0.000) for 1585 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1253 (Rfree = 0.000) for 1582 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1240 (Rfree = 0.000) for 1578 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.86 Search for helices and strands: 0 residues in 0 chains, 1616 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.266 Round 2: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.393 Round 3: 88 peptides, 16 chains. Longest chain 11 peptides. Score 0.391 Round 4: 90 peptides, 15 chains. Longest chain 11 peptides. Score 0.442 Round 5: 91 peptides, 15 chains. Longest chain 10 peptides. Score 0.450 Taking the results from Round 5 Chains 15, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2576 reflections ( 99.27 % complete ) and 3742 restraints for refining 1585 atoms. 3453 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1619 (Rfree = 0.000) for 1585 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.1482 (Rfree = 0.000) for 1582 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.1324 (Rfree = 0.000) for 1579 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.1442 (Rfree = 0.000) for 1576 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.1321 (Rfree = 0.000) for 1577 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.90 Search for helices and strands: 0 residues in 0 chains, 1633 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.324 Round 2: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.373 Round 3: 87 peptides, 14 chains. Longest chain 9 peptides. Score 0.453 Round 4: 84 peptides, 14 chains. Longest chain 9 peptides. Score 0.429 Round 5: 84 peptides, 13 chains. Longest chain 11 peptides. Score 0.464 Taking the results from Round 5 Chains 13, Residues 71, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2576 reflections ( 99.27 % complete ) and 3744 restraints for refining 1585 atoms. 3450 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1776 (Rfree = 0.000) for 1585 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.1437 (Rfree = 0.000) for 1587 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.1411 (Rfree = 0.000) for 1581 atoms. Found 7 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1290 (Rfree = 0.000) for 1583 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1328 (Rfree = 0.000) for 1582 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.84 Search for helices and strands: 0 residues in 0 chains, 1638 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 8 peptides. Score 0.260 Round 2: 77 peptides, 13 chains. Longest chain 12 peptides. Score 0.406 Round 3: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.404 Round 4: 78 peptides, 15 chains. Longest chain 10 peptides. Score 0.340 Round 5: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.407 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 74, 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 2o2x-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2576 reflections ( 99.27 % complete ) and 3737 restraints for refining 1585 atoms. 3457 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1817 (Rfree = 0.000) for 1585 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1500 (Rfree = 0.000) for 1574 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1544 (Rfree = 0.000) for 1567 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1491 (Rfree = 0.000) for 1560 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 28.77