null Sun 23 Dec 22:23:02 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 2pgc-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-3.8-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/2pgc-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-3.8-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 22:23:11 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/2pgc-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-3.8-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 722 and 0 Target number of residues in the AU: 722 Target solvent content: 0.6654 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-3.8-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 8280 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 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: 98.043 3.800 Wilson plot Bfac: 88.94 12038 reflections ( 99.49 % complete ) and 0 restraints for refining 9233 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3459 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3281 (Rfree = 0.000) for 9233 atoms. Found 50 (50 requested) and removed 85 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 9380 seeds are put forward NCS extension: 0 residues added, 9380 seeds are put forward Round 1: 339 peptides, 73 chains. Longest chain 8 peptides. Score 0.247 Round 2: 444 peptides, 75 chains. Longest chain 19 peptides. Score 0.393 Round 3: 492 peptides, 74 chains. Longest chain 15 peptides. Score 0.464 Round 4: 510 peptides, 70 chains. Longest chain 22 peptides. Score 0.508 Round 5: 542 peptides, 74 chains. Longest chain 18 peptides. Score 0.525 Taking the results from Round 5 Chains 76, Residues 468, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17247 restraints for refining 7485 atoms. 15372 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2815 (Rfree = 0.000) for 7485 atoms. Found 26 (41 requested) and removed 59 (20 requested) atoms. Cycle 2: After refmac, R = 0.2613 (Rfree = 0.000) for 7289 atoms. Found 28 (40 requested) and removed 34 (20 requested) atoms. Cycle 3: After refmac, R = 0.2534 (Rfree = 0.000) for 7191 atoms. Found 26 (40 requested) and removed 30 (20 requested) atoms. Cycle 4: After refmac, R = 0.2447 (Rfree = 0.000) for 7120 atoms. Found 22 (39 requested) and removed 31 (19 requested) atoms. Cycle 5: After refmac, R = 0.2387 (Rfree = 0.000) for 7060 atoms. Found 26 (39 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 7269 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7284 seeds are put forward Round 1: 434 peptides, 78 chains. Longest chain 13 peptides. Score 0.361 Round 2: 522 peptides, 76 chains. Longest chain 19 peptides. Score 0.490 Round 3: 530 peptides, 78 chains. Longest chain 17 peptides. Score 0.489 Round 4: 531 peptides, 73 chains. Longest chain 23 peptides. Score 0.518 Round 5: 563 peptides, 79 chains. Longest chain 17 peptides. Score 0.524 Taking the results from Round 5 Chains 79, Residues 484, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17256 restraints for refining 7486 atoms. 15377 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2599 (Rfree = 0.000) for 7486 atoms. Found 41 (41 requested) and removed 87 (20 requested) atoms. Cycle 7: After refmac, R = 0.2456 (Rfree = 0.000) for 7347 atoms. Found 36 (40 requested) and removed 36 (20 requested) atoms. Cycle 8: After refmac, R = 0.2388 (Rfree = 0.000) for 7296 atoms. Found 24 (40 requested) and removed 36 (20 requested) atoms. Cycle 9: After refmac, R = 0.2421 (Rfree = 0.000) for 7251 atoms. Found 29 (40 requested) and removed 29 (20 requested) atoms. Cycle 10: After refmac, R = 0.2308 (Rfree = 0.000) for 7213 atoms. Found 27 (39 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 7415 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 7430 seeds are put forward Round 1: 420 peptides, 80 chains. Longest chain 12 peptides. Score 0.328 Round 2: 513 peptides, 82 chains. Longest chain 12 peptides. Score 0.446 Round 3: 525 peptides, 78 chains. Longest chain 20 peptides. Score 0.483 Round 4: 527 peptides, 81 chains. Longest chain 19 peptides. Score 0.469 Round 5: 544 peptides, 76 chains. Longest chain 29 peptides. Score 0.517 Taking the results from Round 5 Chains 76, Residues 468, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17428 restraints for refining 7488 atoms. 15615 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2422 (Rfree = 0.000) for 7488 atoms. Found 36 (41 requested) and removed 49 (20 requested) atoms. Cycle 12: After refmac, R = 0.2114 (Rfree = 0.000) for 7393 atoms. Found 22 (41 requested) and removed 28 (20 requested) atoms. Cycle 13: After refmac, R = 0.2259 (Rfree = 0.000) for 7344 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Cycle 14: After refmac, R = 0.2046 (Rfree = 0.000) for 7317 atoms. Found 18 (40 requested) and removed 29 (20 requested) atoms. Cycle 15: After refmac, R = 0.1755 (Rfree = 0.000) for 7283 atoms. Found 9 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 7525 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 7547 seeds are put forward Round 1: 454 peptides, 91 chains. Longest chain 13 peptides. Score 0.309 Round 2: 498 peptides, 87 chains. Longest chain 19 peptides. Score 0.396 Round 3: 504 peptides, 81 chains. Longest chain 35 peptides. Score 0.439 Round 4: 496 peptides, 75 chains. Longest chain 29 peptides. Score 0.463 Round 5: 487 peptides, 73 chains. Longest chain 19 peptides. Score 0.463 Taking the results from Round 5 Chains 74, Residues 414, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17276 restraints for refining 7489 atoms. 15633 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2435 (Rfree = 0.000) for 7489 atoms. Found 38 (41 requested) and removed 38 (20 requested) atoms. Cycle 17: After refmac, R = 0.2149 (Rfree = 0.000) for 7432 atoms. Found 21 (41 requested) and removed 24 (20 requested) atoms. Cycle 18: After refmac, R = 0.2242 (Rfree = 0.000) for 7374 atoms. Found 35 (40 requested) and removed 33 (20 requested) atoms. Cycle 19: After refmac, R = 0.1743 (Rfree = 0.000) for 7331 atoms. Found 15 (40 requested) and removed 24 (20 requested) atoms. Cycle 20: After refmac, R = 0.1655 (Rfree = 0.000) for 7307 atoms. Found 3 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 7495 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 7514 seeds are put forward Round 1: 411 peptides, 84 chains. Longest chain 12 peptides. Score 0.289 Round 2: 477 peptides, 81 chains. Longest chain 12 peptides. Score 0.403 Round 3: 478 peptides, 76 chains. Longest chain 14 peptides. Score 0.434 Round 4: 498 peptides, 82 chains. Longest chain 17 peptides. Score 0.426 Round 5: 508 peptides, 82 chains. Longest chain 19 peptides. Score 0.439 Taking the results from Round 5 Chains 82, Residues 426, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17332 restraints for refining 7488 atoms. 15683 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2181 (Rfree = 0.000) for 7488 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. Cycle 22: After refmac, R = 0.2130 (Rfree = 0.000) for 7443 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 23: After refmac, R = 0.2001 (Rfree = 0.000) for 7433 atoms. Found 39 (41 requested) and removed 29 (20 requested) atoms. Cycle 24: After refmac, R = 0.2001 (Rfree = 0.000) for 7421 atoms. Found 35 (40 requested) and removed 23 (20 requested) atoms. Cycle 25: After refmac, R = 0.1917 (Rfree = 0.000) for 7400 atoms. Found 37 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 7692 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7710 seeds are put forward Round 1: 355 peptides, 74 chains. Longest chain 11 peptides. Score 0.267 Round 2: 410 peptides, 72 chains. Longest chain 15 peptides. Score 0.364 Round 3: 432 peptides, 71 chains. Longest chain 21 peptides. Score 0.401 Round 4: 451 peptides, 71 chains. Longest chain 16 peptides. Score 0.427 Round 5: 456 peptides, 70 chains. Longest chain 21 peptides. Score 0.440 Taking the results from Round 5 Chains 71, Residues 386, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17387 restraints for refining 7486 atoms. 15883 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2342 (Rfree = 0.000) for 7486 atoms. Found 41 (41 requested) and removed 36 (20 requested) atoms. Cycle 27: After refmac, R = 0.2092 (Rfree = 0.000) for 7437 atoms. Found 29 (41 requested) and removed 26 (20 requested) atoms. Cycle 28: After refmac, R = 0.2050 (Rfree = 0.000) for 7411 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 29: After refmac, R = 0.1637 (Rfree = 0.000) for 7392 atoms. Found 12 (40 requested) and removed 21 (20 requested) atoms. Cycle 30: After refmac, R = 0.1610 (Rfree = 0.000) for 7361 atoms. Found 10 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 7506 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 7529 seeds are put forward Round 1: 350 peptides, 72 chains. Longest chain 10 peptides. Score 0.272 Round 2: 450 peptides, 82 chains. Longest chain 13 peptides. Score 0.359 Round 3: 425 peptides, 75 chains. Longest chain 16 peptides. Score 0.366 Round 4: 438 peptides, 71 chains. Longest chain 21 peptides. Score 0.409 Round 5: 463 peptides, 73 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 5 Chains 73, Residues 390, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17709 restraints for refining 7489 atoms. 16222 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2383 (Rfree = 0.000) for 7489 atoms. Found 41 (41 requested) and removed 34 (20 requested) atoms. Cycle 32: After refmac, R = 0.2186 (Rfree = 0.000) for 7443 atoms. Found 41 (41 requested) and removed 34 (20 requested) atoms. Cycle 33: After refmac, R = 0.2028 (Rfree = 0.000) for 7409 atoms. Found 33 (40 requested) and removed 25 (20 requested) atoms. Cycle 34: After refmac, R = 0.1688 (Rfree = 0.000) for 7386 atoms. Found 9 (40 requested) and removed 22 (20 requested) atoms. Cycle 35: After refmac, R = 0.1636 (Rfree = 0.000) for 7357 atoms. Found 3 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 7537 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7551 seeds are put forward Round 1: 331 peptides, 68 chains. Longest chain 10 peptides. Score 0.269 Round 2: 376 peptides, 65 chains. Longest chain 13 peptides. Score 0.358 Round 3: 375 peptides, 61 chains. Longest chain 12 peptides. Score 0.383 Round 4: 400 peptides, 66 chains. Longest chain 12 peptides. Score 0.387 Round 5: 369 peptides, 61 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 4 Chains 66, Residues 334, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17854 restraints for refining 7488 atoms. 16584 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2148 (Rfree = 0.000) for 7488 atoms. Found 29 (41 requested) and removed 34 (20 requested) atoms. Cycle 37: After refmac, R = 0.2123 (Rfree = 0.000) for 7452 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. Cycle 38: After refmac, R = 0.2127 (Rfree = 0.000) for 7441 atoms. Found 34 (41 requested) and removed 33 (20 requested) atoms. Cycle 39: After refmac, R = 0.2066 (Rfree = 0.000) for 7422 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Cycle 40: After refmac, R = 0.1679 (Rfree = 0.000) for 7415 atoms. Found 10 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 7605 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7618 seeds are put forward Round 1: 306 peptides, 64 chains. Longest chain 11 peptides. Score 0.255 Round 2: 383 peptides, 68 chains. Longest chain 15 peptides. Score 0.349 Round 3: 384 peptides, 66 chains. Longest chain 15 peptides. Score 0.364 Round 4: 382 peptides, 67 chains. Longest chain 14 peptides. Score 0.354 Round 5: 381 peptides, 64 chains. Longest chain 15 peptides. Score 0.372 Taking the results from Round 5 Chains 65, Residues 317, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12038 reflections ( 99.49 % complete ) and 17679 restraints for refining 7489 atoms. 16441 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2324 (Rfree = 0.000) for 7489 atoms. Found 41 (41 requested) and removed 36 (20 requested) atoms. Cycle 42: After refmac, R = 0.2141 (Rfree = 0.000) for 7461 atoms. Found 41 (41 requested) and removed 28 (20 requested) atoms. Cycle 43: After refmac, R = 0.2088 (Rfree = 0.000) for 7440 atoms. Found 41 (41 requested) and removed 21 (20 requested) atoms. Cycle 44: After refmac, R = 0.2079 (Rfree = 0.000) for 7427 atoms. Found 41 (41 requested) and removed 29 (20 requested) atoms. Cycle 45: After refmac, R = 0.2023 (Rfree = 0.000) for 7426 atoms. Found 39 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 7643 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 7655 seeds are put forward Round 1: 239 peptides, 54 chains. Longest chain 9 peptides. Score 0.211 Round 2: 298 peptides, 61 chains. Longest chain 18 peptides. Score 0.263 Round 3: 295 peptides, 59 chains. Longest chain 9 peptides. Score 0.272 Round 4: 293 peptides, 57 chains. Longest chain 12 peptides. Score 0.283 Round 5: 313 peptides, 55 chains. Longest chain 13 peptides. Score 0.329 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 258, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2pgc-3_warpNtrace.pdb as input Building loops using Loopy2018 55 chains (258 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12038 reflections ( 99.49 % complete ) and 17378 restraints for refining 7324 atoms. 16372 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2257 (Rfree = 0.000) for 7324 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2229 (Rfree = 0.000) for 7262 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2248 (Rfree = 0.000) for 7210 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2274 (Rfree = 0.000) for 7169 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:57:53 GMT 2018 Job finished. TimeTaking 94.85 Used memory is bytes: 21002640