null Sun 23 Dec 22:23:07 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 2ooc-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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/2ooc-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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 22:23:16 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/2ooc-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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 166 and 0 Target number of residues in the AU: 166 Target solvent content: 0.6555 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.53 Input MTZ file: 2ooc-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: 154 Cell parameters: 62.597 62.597 115.277 90.000 90.000 120.000 Input sequence file: 2ooc-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1808 target number of atoms Had to go as low as 0.70 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: 54.211 3.602 Wilson plot Bfac: 81.79 3282 reflections ( 99.73 % complete ) and 0 restraints for refining 2019 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3390 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3190 (Rfree = 0.000) for 2019 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 2090 seeds are put forward NCS extension: 0 residues added, 2090 seeds are put forward Round 1: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.399 Round 2: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.427 Round 3: 103 peptides, 14 chains. Longest chain 12 peptides. Score 0.488 Round 4: 107 peptides, 12 chains. Longest chain 24 peptides. Score 0.559 Round 5: 118 peptides, 17 chains. Longest chain 13 peptides. Score 0.497 Taking the results from Round 4 Chains 13, Residues 95, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3282 reflections ( 99.73 % complete ) and 3808 restraints for refining 1636 atoms. 3413 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2491 (Rfree = 0.000) for 1636 atoms. Found 2 (10 requested) and removed 18 (5 requested) atoms. Cycle 2: After refmac, R = 0.2462 (Rfree = 0.000) for 1591 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.2391 (Rfree = 0.000) for 1588 atoms. Found 0 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2390 (Rfree = 0.000) for 1575 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2371 (Rfree = 0.000) for 1569 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 1639 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1659 seeds are put forward Round 1: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.385 Round 2: 112 peptides, 15 chains. Longest chain 13 peptides. Score 0.513 Round 3: 108 peptides, 14 chains. Longest chain 15 peptides. Score 0.516 Round 4: 118 peptides, 14 chains. Longest chain 14 peptides. Score 0.568 Round 5: 119 peptides, 15 chains. Longest chain 15 peptides. Score 0.550 Taking the results from Round 4 Chains 15, Residues 104, Estimated correctness of the model 1.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3282 reflections ( 99.73 % complete ) and 3460 restraints for refining 1535 atoms. 3025 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2634 (Rfree = 0.000) for 1535 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 7: After refmac, R = 0.2522 (Rfree = 0.000) for 1527 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 8: After refmac, R = 0.2464 (Rfree = 0.000) for 1522 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2410 (Rfree = 0.000) for 1519 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2384 (Rfree = 0.000) for 1514 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 1588 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 1590 seeds are put forward Round 1: 113 peptides, 16 chains. Longest chain 16 peptides. Score 0.494 Round 2: 114 peptides, 14 chains. Longest chain 15 peptides. Score 0.548 Round 3: 118 peptides, 14 chains. Longest chain 19 peptides. Score 0.568 Round 4: 112 peptides, 16 chains. Longest chain 14 peptides. Score 0.489 Round 5: 120 peptides, 15 chains. Longest chain 17 peptides. Score 0.555 Taking the results from Round 3 Chains 14, Residues 104, Estimated correctness of the model 1.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3282 reflections ( 99.73 % complete ) and 3459 restraints for refining 1507 atoms. 3057 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2551 (Rfree = 0.000) for 1507 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 12: After refmac, R = 0.2459 (Rfree = 0.000) for 1504 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2411 (Rfree = 0.000) for 1505 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2351 (Rfree = 0.000) for 1505 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2336 (Rfree = 0.000) for 1500 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 1557 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1577 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.329 Round 2: 89 peptides, 13 chains. Longest chain 11 peptides. Score 0.433 Round 3: 95 peptides, 14 chains. Longest chain 17 peptides. Score 0.442 Round 4: 105 peptides, 13 chains. Longest chain 19 peptides. Score 0.524 Round 5: 105 peptides, 14 chains. Longest chain 21 peptides. Score 0.500 Taking the results from Round 4 Chains 15, Residues 92, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3282 reflections ( 99.73 % complete ) and 3491 restraints for refining 1553 atoms. 3085 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2690 (Rfree = 0.000) for 1553 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 17: After refmac, R = 0.2550 (Rfree = 0.000) for 1549 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.2485 (Rfree = 0.000) for 1551 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2447 (Rfree = 0.000) for 1550 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2407 (Rfree = 0.000) for 1544 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 1634 seeds are put forward NCS extension: 0 residues added, 1634 seeds are put forward Round 1: 87 peptides, 15 chains. Longest chain 11 peptides. Score 0.364 Round 2: 104 peptides, 16 chains. Longest chain 12 peptides. Score 0.443 Round 3: 98 peptides, 14 chains. Longest chain 13 peptides. Score 0.460 Round 4: 102 peptides, 15 chains. Longest chain 17 peptides. Score 0.457 Round 5: 104 peptides, 15 chains. Longest chain 13 peptides. Score 0.469 Taking the results from Round 5 Chains 15, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3282 reflections ( 99.73 % complete ) and 3643 restraints for refining 1558 atoms. 3302 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2868 (Rfree = 0.000) for 1558 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 22: After refmac, R = 0.2734 (Rfree = 0.000) for 1561 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 23: After refmac, R = 0.2648 (Rfree = 0.000) for 1560 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2604 (Rfree = 0.000) for 1556 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2557 (Rfree = 0.000) for 1551 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 1633 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 1647 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.305 Round 2: 104 peptides, 20 chains. Longest chain 7 peptides. Score 0.335 Round 3: 100 peptides, 15 chains. Longest chain 14 peptides. Score 0.445 Round 4: 102 peptides, 15 chains. Longest chain 13 peptides. Score 0.457 Round 5: 103 peptides, 14 chains. Longest chain 17 peptides. Score 0.488 Taking the results from Round 5 Chains 14, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3282 reflections ( 99.73 % complete ) and 3629 restraints for refining 1543 atoms. 3287 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2764 (Rfree = 0.000) for 1543 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 27: After refmac, R = 0.2597 (Rfree = 0.000) for 1539 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 28: After refmac, R = 0.2515 (Rfree = 0.000) for 1536 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2452 (Rfree = 0.000) for 1535 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2406 (Rfree = 0.000) for 1533 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 1584 seeds are put forward NCS extension: 0 residues added, 1584 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 9 peptides. Score 0.273 Round 2: 96 peptides, 17 chains. Longest chain 13 peptides. Score 0.366 Round 3: 86 peptides, 14 chains. Longest chain 13 peptides. Score 0.386 Round 4: 83 peptides, 13 chains. Longest chain 14 peptides. Score 0.395 Round 5: 82 peptides, 13 chains. Longest chain 9 peptides. Score 0.389 Taking the results from Round 4 Chains 13, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3282 reflections ( 99.73 % complete ) and 3804 restraints for refining 1548 atoms. 3537 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2592 (Rfree = 0.000) for 1548 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2375 (Rfree = 0.000) for 1547 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2377 (Rfree = 0.000) for 1543 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2307 (Rfree = 0.000) for 1543 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2286 (Rfree = 0.000) for 1536 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 1597 seeds are put forward NCS extension: 0 residues added, 1597 seeds are put forward Round 1: 90 peptides, 17 chains. Longest chain 10 peptides. Score 0.327 Round 2: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.342 Round 3: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.380 Round 4: 94 peptides, 14 chains. Longest chain 13 peptides. Score 0.436 Round 5: 89 peptides, 14 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 4 Chains 14, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3282 reflections ( 99.73 % complete ) and 3714 restraints for refining 1553 atoms. 3408 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2555 (Rfree = 0.000) for 1553 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 37: After refmac, R = 0.2525 (Rfree = 0.000) for 1549 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.2405 (Rfree = 0.000) for 1547 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2406 (Rfree = 0.000) for 1543 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2384 (Rfree = 0.000) for 1540 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 1614 seeds are put forward NCS extension: 9 residues added (2 deleted due to clashes), 1623 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.298 Round 2: 74 peptides, 11 chains. Longest chain 11 peptides. Score 0.396 Round 3: 82 peptides, 12 chains. Longest chain 17 peptides. Score 0.418 Round 4: 87 peptides, 14 chains. Longest chain 13 peptides. Score 0.393 Round 5: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.351 Taking the results from Round 3 Chains 12, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3282 reflections ( 99.73 % complete ) and 3784 restraints for refining 1550 atoms. 3516 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2529 (Rfree = 0.000) for 1550 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2344 (Rfree = 0.000) for 1549 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 43: After refmac, R = 0.2295 (Rfree = 0.000) for 1541 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.2128 (Rfree = 0.000) for 1534 atoms. Found 0 (9 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.2110 (Rfree = 0.000) for 1527 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 1599 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1620 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.256 Round 2: 79 peptides, 12 chains. Longest chain 16 peptides. Score 0.399 Round 3: 84 peptides, 16 chains. Longest chain 12 peptides. Score 0.315 Round 4: 79 peptides, 14 chains. Longest chain 11 peptides. Score 0.340 Round 5: 86 peptides, 13 chains. Longest chain 18 peptides. Score 0.414 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 73, 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 2ooc-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3282 reflections ( 99.73 % complete ) and 3548 restraints for refining 1506 atoms. 3269 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2287 (Rfree = 0.000) for 1506 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2249 (Rfree = 0.000) for 1497 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2247 (Rfree = 0.000) for 1493 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2217 (Rfree = 0.000) for 1487 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:03 GMT 2018 Job finished. TimeTaking 29.93 Used memory is bytes: 4319104