Sun 23 Dec 22:23:13 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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/2ooc-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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 22:23:22 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6431 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-3.4-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: 154 Cell parameters: 62.597 62.597 115.277 90.000 90.000 120.000 Input sequence file: 2ooc-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1808 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 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 3.400 Wilson plot Bfac: 73.43 3879 reflections ( 99.77 % complete ) and 0 restraints for refining 2006 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3388 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3174 (Rfree = 0.000) for 2006 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 2063 seeds are put forward NCS extension: 0 residues added, 2063 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 10 peptides. Score 0.322 Round 2: 109 peptides, 17 chains. Longest chain 15 peptides. Score 0.446 Round 3: 109 peptides, 16 chains. Longest chain 15 peptides. Score 0.472 Round 4: 109 peptides, 17 chains. Longest chain 15 peptides. Score 0.446 Round 5: 100 peptides, 14 chains. Longest chain 12 peptides. Score 0.471 Taking the results from Round 3 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3866 restraints for refining 1639 atoms. 3487 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2520 (Rfree = 0.000) for 1639 atoms. Found 3 (12 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.2401 (Rfree = 0.000) for 1604 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.2357 (Rfree = 0.000) for 1585 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2292 (Rfree = 0.000) for 1568 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.2254 (Rfree = 0.000) for 1553 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 1665 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1682 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.359 Round 2: 120 peptides, 16 chains. Longest chain 12 peptides. Score 0.532 Round 3: 130 peptides, 20 chains. Longest chain 14 peptides. Score 0.491 Round 4: 120 peptides, 18 chains. Longest chain 12 peptides. Score 0.484 Round 5: 115 peptides, 16 chains. Longest chain 25 peptides. Score 0.505 Taking the results from Round 2 Chains 16, Residues 104, Estimated correctness of the model 4.9 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3540 restraints for refining 1564 atoms. 3126 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2558 (Rfree = 0.000) for 1564 atoms. Found 6 (11 requested) and removed 13 (5 requested) atoms. Cycle 7: After refmac, R = 0.2494 (Rfree = 0.000) for 1539 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2494 (Rfree = 0.000) for 1532 atoms. Found 8 (11 requested) and removed 12 (5 requested) atoms. Cycle 9: After refmac, R = 0.2425 (Rfree = 0.000) for 1522 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.2317 (Rfree = 0.000) for 1517 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 1608 seeds are put forward NCS extension: 0 residues added, 1608 seeds are put forward Round 1: 103 peptides, 20 chains. Longest chain 11 peptides. Score 0.329 Round 2: 119 peptides, 17 chains. Longest chain 12 peptides. Score 0.503 Round 3: 122 peptides, 12 chains. Longest chain 25 peptides. Score 0.630 Round 4: 108 peptides, 14 chains. Longest chain 15 peptides. Score 0.516 Round 5: 121 peptides, 18 chains. Longest chain 14 peptides. Score 0.489 Taking the results from Round 3 Chains 14, Residues 110, Estimated correctness of the model 38.2 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3257 restraints for refining 1570 atoms. 2772 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2616 (Rfree = 0.000) for 1570 atoms. Found 11 (11 requested) and removed 25 (5 requested) atoms. Cycle 12: After refmac, R = 0.2455 (Rfree = 0.000) for 1549 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 13: After refmac, R = 0.2382 (Rfree = 0.000) for 1539 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 14: After refmac, R = 0.2411 (Rfree = 0.000) for 1530 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2273 (Rfree = 0.000) for 1524 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.34 Search for helices and strands: 0 residues in 0 chains, 1607 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 1635 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 11 peptides. Score 0.317 Round 2: 119 peptides, 16 chains. Longest chain 15 peptides. Score 0.526 Round 3: 123 peptides, 16 chains. Longest chain 17 peptides. Score 0.547 Round 4: 124 peptides, 17 chains. Longest chain 13 peptides. Score 0.529 Round 5: 126 peptides, 16 chains. Longest chain 25 peptides. Score 0.562 Taking the results from Round 5 Chains 16, Residues 110, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3432 restraints for refining 1565 atoms. 3008 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2495 (Rfree = 0.000) for 1565 atoms. Found 7 (11 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.2495 (Rfree = 0.000) for 1545 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.2409 (Rfree = 0.000) for 1542 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2372 (Rfree = 0.000) for 1535 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2335 (Rfree = 0.000) for 1532 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.33 Search for helices and strands: 0 residues in 0 chains, 1643 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 1664 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.276 Round 2: 102 peptides, 18 chains. Longest chain 8 peptides. Score 0.377 Round 3: 104 peptides, 16 chains. Longest chain 10 peptides. Score 0.443 Round 4: 115 peptides, 17 chains. Longest chain 18 peptides. Score 0.480 Round 5: 112 peptides, 16 chains. Longest chain 14 peptides. Score 0.489 Taking the results from Round 5 Chains 16, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3536 restraints for refining 1579 atoms. 3168 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2723 (Rfree = 0.000) for 1579 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 22: After refmac, R = 0.2495 (Rfree = 0.000) for 1572 atoms. Found 2 (11 requested) and removed 12 (5 requested) atoms. Cycle 23: After refmac, R = 0.2371 (Rfree = 0.000) for 1556 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.2324 (Rfree = 0.000) for 1546 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2300 (Rfree = 0.000) for 1544 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 1652 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1672 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 12 peptides. Score 0.335 Round 2: 106 peptides, 18 chains. Longest chain 9 peptides. Score 0.402 Round 3: 115 peptides, 18 chains. Longest chain 10 peptides. Score 0.456 Round 4: 125 peptides, 21 chains. Longest chain 12 peptides. Score 0.438 Round 5: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.432 Taking the results from Round 3 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3641 restraints for refining 1608 atoms. 3271 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2490 (Rfree = 0.000) for 1608 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.2352 (Rfree = 0.000) for 1603 atoms. Found 11 (12 requested) and removed 10 (6 requested) atoms. Cycle 28: After refmac, R = 0.2255 (Rfree = 0.000) for 1600 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2212 (Rfree = 0.000) for 1595 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2216 (Rfree = 0.000) for 1586 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 1675 seeds are put forward NCS extension: 0 residues added, 1675 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.286 Round 2: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.349 Round 3: 98 peptides, 16 chains. Longest chain 14 peptides. Score 0.406 Round 4: 110 peptides, 18 chains. Longest chain 10 peptides. Score 0.426 Round 5: 95 peptides, 16 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 4 Chains 18, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3702 restraints for refining 1635 atoms. 3352 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2503 (Rfree = 0.000) for 1635 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 32: After refmac, R = 0.2291 (Rfree = 0.000) for 1629 atoms. Found 0 (12 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2267 (Rfree = 0.000) for 1619 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.2234 (Rfree = 0.000) for 1613 atoms. Found 0 (12 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.2215 (Rfree = 0.000) for 1603 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 1662 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 1664 seeds are put forward Round 1: 74 peptides, 14 chains. Longest chain 10 peptides. Score 0.305 Round 2: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.335 Round 3: 85 peptides, 16 chains. Longest chain 10 peptides. Score 0.322 Round 4: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.388 Round 5: 100 peptides, 15 chains. Longest chain 19 peptides. Score 0.445 Taking the results from Round 5 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3707 restraints for refining 1643 atoms. 3364 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2423 (Rfree = 0.000) for 1643 atoms. Found 3 (12 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.2368 (Rfree = 0.000) for 1631 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2439 (Rfree = 0.000) for 1624 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.2448 (Rfree = 0.000) for 1617 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2402 (Rfree = 0.000) for 1613 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.21 Search for helices and strands: 0 residues in 0 chains, 1664 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 1693 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.281 Round 2: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.315 Round 3: 83 peptides, 16 chains. Longest chain 12 peptides. Score 0.308 Round 4: 73 peptides, 12 chains. Longest chain 11 peptides. Score 0.359 Round 5: 81 peptides, 14 chains. Longest chain 9 peptides. Score 0.353 Taking the results from Round 4 Chains 12, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.77 % complete ) and 3942 restraints for refining 1644 atoms. 3710 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2391 (Rfree = 0.000) for 1644 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2329 (Rfree = 0.000) for 1641 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2315 (Rfree = 0.000) for 1635 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2252 (Rfree = 0.000) for 1628 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2250 (Rfree = 0.000) for 1625 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.22 Search for helices and strands: 0 residues in 0 chains, 1712 seeds are put forward NCS extension: 0 residues added, 1712 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 8 peptides. Score 0.263 Round 2: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.329 Round 3: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.324 Round 4: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.319 Round 5: 78 peptides, 12 chains. Longest chain 10 peptides. Score 0.392 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 66, 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. 3879 reflections ( 99.77 % complete ) and 3845 restraints for refining 1643 atoms. 3593 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2569 (Rfree = 0.000) for 1643 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2414 (Rfree = 0.000) for 1635 atoms. Found 0 (12 requested) and removed 3 (6 requested) atoms. Cycle 48: After refmac, R = 0.2425 (Rfree = 0.000) for 1632 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2346 (Rfree = 0.000) for 1624 atoms. TimeTaking 30.57