Sun 23 Dec 22:23:05 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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/2ooc-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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 22:23:15 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-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 153 and 0 Target number of residues in the AU: 153 Target solvent content: 0.6825 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-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: 154 Cell parameters: 62.597 62.597 115.277 90.000 90.000 120.000 Input sequence file: 2ooc-4.0-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 4.000 Wilson plot Bfac: 102.83 Failed to save intermediate PDB 2434 reflections ( 99.67 % complete ) and 0 restraints for refining 1993 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3553 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3311 (Rfree = 0.000) for 1993 atoms. Found 9 (9 requested) and removed 30 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.97 3.81 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 0 residues added, 2035 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.266 Round 2: 82 peptides, 13 chains. Longest chain 14 peptides. Score 0.389 Round 3: 84 peptides, 12 chains. Longest chain 13 peptides. Score 0.430 Round 4: 87 peptides, 12 chains. Longest chain 14 peptides. Score 0.448 Round 5: 83 peptides, 10 chains. Longest chain 13 peptides. Score 0.480 Taking the results from Round 5 Chains 10, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 4105 restraints for refining 1625 atoms. 3823 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2460 (Rfree = 0.000) for 1625 atoms. Found 5 (7 requested) and removed 21 (3 requested) atoms. Cycle 2: After refmac, R = 0.2462 (Rfree = 0.000) for 1580 atoms. Found 2 (7 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.2431 (Rfree = 0.000) for 1572 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2482 (Rfree = 0.000) for 1567 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2500 (Rfree = 0.000) for 1560 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.00 3.84 Search for helices and strands: 0 residues in 0 chains, 1630 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1646 seeds are put forward Round 1: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.333 Round 2: 84 peptides, 11 chains. Longest chain 16 peptides. Score 0.458 Round 3: 82 peptides, 12 chains. Longest chain 13 peptides. Score 0.418 Round 4: 83 peptides, 10 chains. Longest chain 14 peptides. Score 0.480 Round 5: 82 peptides, 10 chains. Longest chain 14 peptides. Score 0.474 Taking the results from Round 4 Chains 10, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3890 restraints for refining 1550 atoms. 3608 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2392 (Rfree = 0.000) for 1550 atoms. Found 5 (7 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.2263 (Rfree = 0.000) for 1531 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.2334 (Rfree = 0.000) for 1524 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.2235 (Rfree = 0.000) for 1521 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. Cycle 10: After refmac, R = 0.2209 (Rfree = 0.000) for 1515 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.00 3.84 Search for helices and strands: 0 residues in 0 chains, 1594 seeds are put forward NCS extension: 0 residues added, 1594 seeds are put forward Round 1: 82 peptides, 16 chains. Longest chain 10 peptides. Score 0.301 Round 2: 89 peptides, 13 chains. Longest chain 15 peptides. Score 0.433 Round 3: 89 peptides, 10 chains. Longest chain 17 peptides. Score 0.514 Round 4: 83 peptides, 12 chains. Longest chain 16 peptides. Score 0.424 Round 5: 90 peptides, 12 chains. Longest chain 13 peptides. Score 0.466 Taking the results from Round 3 Chains 10, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3808 restraints for refining 1545 atoms. 3502 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2288 (Rfree = 0.000) for 1545 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 12: After refmac, R = 0.2229 (Rfree = 0.000) for 1523 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.2020 (Rfree = 0.000) for 1513 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2138 (Rfree = 0.000) for 1505 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 15: After refmac, R = 0.1934 (Rfree = 0.000) for 1494 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.99 3.83 Search for helices and strands: 0 residues in 0 chains, 1566 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1587 seeds are put forward Round 1: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.317 Round 2: 83 peptides, 12 chains. Longest chain 14 peptides. Score 0.424 Round 3: 88 peptides, 16 chains. Longest chain 11 peptides. Score 0.342 Round 4: 77 peptides, 14 chains. Longest chain 10 peptides. Score 0.326 Round 5: 85 peptides, 13 chains. Longest chain 14 peptides. Score 0.408 Taking the results from Round 2 Chains 12, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3645 restraints for refining 1494 atoms. 3373 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2302 (Rfree = 0.000) for 1494 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 17: After refmac, R = 0.2233 (Rfree = 0.000) for 1477 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.2385 (Rfree = 0.000) for 1465 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.2218 (Rfree = 0.000) for 1459 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2281 (Rfree = 0.000) for 1452 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.00 3.84 Search for helices and strands: 0 residues in 0 chains, 1544 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1569 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 9 peptides. Score 0.286 Round 2: 82 peptides, 14 chains. Longest chain 13 peptides. Score 0.360 Round 3: 84 peptides, 13 chains. Longest chain 10 peptides. Score 0.402 Round 4: 86 peptides, 12 chains. Longest chain 11 peptides. Score 0.442 Round 5: 96 peptides, 15 chains. Longest chain 12 peptides. Score 0.421 Taking the results from Round 4 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3539 restraints for refining 1478 atoms. 3255 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2478 (Rfree = 0.000) for 1478 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 22: After refmac, R = 0.2414 (Rfree = 0.000) for 1457 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2388 (Rfree = 0.000) for 1454 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.2484 (Rfree = 0.000) for 1449 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. Cycle 25: After refmac, R = 0.2568 (Rfree = 0.000) for 1442 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.99 3.83 Search for helices and strands: 0 residues in 0 chains, 1500 seeds are put forward NCS extension: 0 residues added, 1500 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.303 Round 2: 88 peptides, 15 chains. Longest chain 13 peptides. Score 0.371 Round 3: 85 peptides, 12 chains. Longest chain 18 peptides. Score 0.436 Round 4: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.392 Round 5: 92 peptides, 13 chains. Longest chain 17 peptides. Score 0.451 Taking the results from Round 5 Chains 13, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3350 restraints for refining 1451 atoms. 3047 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2492 (Rfree = 0.000) for 1451 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.2327 (Rfree = 0.000) for 1437 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.2250 (Rfree = 0.000) for 1434 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.2201 (Rfree = 0.000) for 1431 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.2113 (Rfree = 0.000) for 1427 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.96 3.80 Search for helices and strands: 0 residues in 0 chains, 1494 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 1523 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.284 Round 2: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.344 Round 3: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.331 Round 4: 82 peptides, 12 chains. Longest chain 16 peptides. Score 0.418 Round 5: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.358 Taking the results from Round 4 Chains 13, Residues 70, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3517 restraints for refining 1475 atoms. 3210 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2359 (Rfree = 0.000) for 1475 atoms. Found 3 (7 requested) and removed 12 (3 requested) atoms. Cycle 32: After refmac, R = 0.2516 (Rfree = 0.000) for 1454 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. Cycle 33: After refmac, R = 0.2556 (Rfree = 0.000) for 1444 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 34: After refmac, R = 0.2352 (Rfree = 0.000) for 1423 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 35: After refmac, R = 0.2256 (Rfree = 0.000) for 1394 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.98 3.82 Search for helices and strands: 0 residues in 0 chains, 1489 seeds are put forward NCS extension: 0 residues added, 1489 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.226 Round 2: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.308 Round 3: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Round 4: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.347 Round 5: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.298 Taking the results from Round 4 Chains 14, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3499 restraints for refining 1432 atoms. 3249 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2546 (Rfree = 0.000) for 1432 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 37: After refmac, R = 0.2516 (Rfree = 0.000) for 1399 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 38: After refmac, R = 0.2486 (Rfree = 0.000) for 1380 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 39: After refmac, R = 0.2673 (Rfree = 0.000) for 1376 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 40: After refmac, R = 0.2404 (Rfree = 0.000) for 1357 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.94 3.79 Search for helices and strands: 0 residues in 0 chains, 1465 seeds are put forward NCS extension: 0 residues added, 1465 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 5 peptides. Score 0.193 Round 2: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.250 Round 3: 64 peptides, 14 chains. Longest chain 6 peptides. Score 0.231 Round 4: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.281 Round 5: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.296 Taking the results from Round 5 Chains 12, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3306 restraints for refining 1355 atoms. 3110 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2594 (Rfree = 0.000) for 1355 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 42: After refmac, R = 0.2549 (Rfree = 0.000) for 1334 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 43: After refmac, R = 0.2550 (Rfree = 0.000) for 1319 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 44: After refmac, R = 0.2465 (Rfree = 0.000) for 1306 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 45: After refmac, R = 0.2652 (Rfree = 0.000) for 1299 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.94 3.79 Search for helices and strands: 0 residues in 0 chains, 1373 seeds are put forward NCS extension: 0 residues added, 1373 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.213 Round 2: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.255 Round 3: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.256 Round 4: 67 peptides, 13 chains. Longest chain 10 peptides. Score 0.286 Round 5: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.233 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 54, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2434 reflections ( 99.67 % complete ) and 3120 restraints for refining 1318 atoms. 2917 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2608 (Rfree = 0.000) for 1318 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2500 (Rfree = 0.000) for 1297 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2421 (Rfree = 0.000) for 1286 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2372 (Rfree = 0.000) for 1280 atoms. TimeTaking 28.77