null Sun 23 Dec 22:22:46 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-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/2pgc-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-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 22:22:56 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-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 742 and 0 Target number of residues in the AU: 742 Target solvent content: 0.6561 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-3.6-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-3.6-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 3.600 Wilson plot Bfac: 82.18 14118 reflections ( 99.56 % complete ) and 0 restraints for refining 9160 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3411 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3334 (Rfree = 0.000) for 9160 atoms. Found 58 (58 requested) and removed 65 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 9347 seeds are put forward NCS extension: 0 residues added, 9347 seeds are put forward Round 1: 390 peptides, 81 chains. Longest chain 11 peptides. Score 0.276 Round 2: 494 peptides, 85 chains. Longest chain 25 peptides. Score 0.403 Round 3: 540 peptides, 76 chains. Longest chain 27 peptides. Score 0.512 Round 4: 558 peptides, 74 chains. Longest chain 27 peptides. Score 0.544 Round 5: 573 peptides, 76 chains. Longest chain 24 peptides. Score 0.551 Taking the results from Round 5 Chains 76, Residues 497, Estimated correctness of the model 0.0 % 6 chains (49 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 16845 restraints for refining 7501 atoms. 14776 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2885 (Rfree = 0.000) for 7501 atoms. Found 39 (48 requested) and removed 54 (24 requested) atoms. Cycle 2: After refmac, R = 0.2481 (Rfree = 0.000) for 7366 atoms. Found 30 (48 requested) and removed 35 (24 requested) atoms. Cycle 3: After refmac, R = 0.2328 (Rfree = 0.000) for 7284 atoms. Found 16 (47 requested) and removed 30 (23 requested) atoms. Cycle 4: After refmac, R = 0.2218 (Rfree = 0.000) for 7245 atoms. Found 15 (46 requested) and removed 31 (23 requested) atoms. Cycle 5: After refmac, R = 0.2180 (Rfree = 0.000) for 7220 atoms. Found 9 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 7469 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 7484 seeds are put forward Round 1: 515 peptides, 81 chains. Longest chain 22 peptides. Score 0.454 Round 2: 593 peptides, 79 chains. Longest chain 23 peptides. Score 0.558 Round 3: 580 peptides, 74 chains. Longest chain 26 peptides. Score 0.568 Round 4: 572 peptides, 78 chains. Longest chain 23 peptides. Score 0.539 Round 5: 587 peptides, 75 chains. Longest chain 19 peptides. Score 0.571 Taking the results from Round 5 Chains 75, Residues 512, Estimated correctness of the model 3.0 % 3 chains (48 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 16259 restraints for refining 7506 atoms. 14052 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2508 (Rfree = 0.000) for 7506 atoms. Found 37 (48 requested) and removed 84 (24 requested) atoms. Cycle 7: After refmac, R = 0.2284 (Rfree = 0.000) for 7408 atoms. Found 18 (47 requested) and removed 27 (23 requested) atoms. Cycle 8: After refmac, R = 0.2273 (Rfree = 0.000) for 7384 atoms. Found 12 (47 requested) and removed 25 (23 requested) atoms. Cycle 9: After refmac, R = 0.2303 (Rfree = 0.000) for 7370 atoms. Found 7 (47 requested) and removed 24 (23 requested) atoms. Cycle 10: After refmac, R = 0.2292 (Rfree = 0.000) for 7351 atoms. Found 5 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 7539 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 7554 seeds are put forward Round 1: 479 peptides, 83 chains. Longest chain 13 peptides. Score 0.394 Round 2: 522 peptides, 78 chains. Longest chain 18 peptides. Score 0.479 Round 3: 541 peptides, 77 chains. Longest chain 17 peptides. Score 0.508 Round 4: 545 peptides, 80 chains. Longest chain 17 peptides. Score 0.497 Round 5: 555 peptides, 78 chains. Longest chain 18 peptides. Score 0.520 Taking the results from Round 5 Chains 80, Residues 477, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17164 restraints for refining 7504 atoms. 15268 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2660 (Rfree = 0.000) for 7504 atoms. Found 40 (48 requested) and removed 35 (24 requested) atoms. Cycle 12: After refmac, R = 0.2298 (Rfree = 0.000) for 7460 atoms. Found 25 (48 requested) and removed 63 (24 requested) atoms. Cycle 13: After refmac, R = 0.2319 (Rfree = 0.000) for 7403 atoms. Found 10 (47 requested) and removed 26 (23 requested) atoms. Cycle 14: After refmac, R = 0.2300 (Rfree = 0.000) for 7384 atoms. Found 6 (47 requested) and removed 26 (23 requested) atoms. Cycle 15: After refmac, R = 0.2316 (Rfree = 0.000) for 7362 atoms. Found 8 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 7577 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 7598 seeds are put forward Round 1: 470 peptides, 84 chains. Longest chain 14 peptides. Score 0.375 Round 2: 526 peptides, 81 chains. Longest chain 14 peptides. Score 0.468 Round 3: 532 peptides, 73 chains. Longest chain 18 peptides. Score 0.519 Round 4: 509 peptides, 71 chains. Longest chain 17 peptides. Score 0.502 Round 5: 518 peptides, 73 chains. Longest chain 17 peptides. Score 0.502 Taking the results from Round 3 Chains 73, Residues 459, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ *** WARNING *** Conditional restraints for refinement could not be generated 14118 reflections ( 99.56 % complete ) and 1764 restraints for refining 7506 atoms. 1 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2171 (Rfree = 0.000) for 7506 atoms. Found 27 (48 requested) and removed 46 (24 requested) atoms. Cycle 17: After refmac, R = 0.2026 (Rfree = 0.000) for 7451 atoms. Found 23 (48 requested) and removed 26 (24 requested) atoms. Cycle 18: After refmac, R = 0.1987 (Rfree = 0.000) for 7431 atoms. Found 7 (47 requested) and removed 23 (23 requested) atoms. Cycle 19: After refmac, R = 0.1980 (Rfree = 0.000) for 7410 atoms. Found 2 (47 requested) and removed 23 (23 requested) atoms. Cycle 20: After refmac, R = 0.1989 (Rfree = 0.000) for 7386 atoms. Found 1 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 7623 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 7643 seeds are put forward Round 1: 459 peptides, 85 chains. Longest chain 12 peptides. Score 0.354 Round 2: 499 peptides, 76 chains. Longest chain 16 peptides. Score 0.461 Round 3: 505 peptides, 71 chains. Longest chain 21 peptides. Score 0.497 Round 4: 522 peptides, 74 chains. Longest chain 18 peptides. Score 0.501 Round 5: 508 peptides, 74 chains. Longest chain 22 peptides. Score 0.484 Taking the results from Round 4 Chains 74, Residues 448, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17556 restraints for refining 7506 atoms. 15838 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2312 (Rfree = 0.000) for 7506 atoms. Found 33 (48 requested) and removed 30 (24 requested) atoms. Cycle 22: After refmac, R = 0.2050 (Rfree = 0.000) for 7467 atoms. Found 15 (48 requested) and removed 25 (24 requested) atoms. Cycle 23: After refmac, R = 0.2005 (Rfree = 0.000) for 7443 atoms. Found 10 (47 requested) and removed 23 (23 requested) atoms. Cycle 24: After refmac, R = 0.1999 (Rfree = 0.000) for 7427 atoms. Found 8 (47 requested) and removed 24 (23 requested) atoms. Cycle 25: After refmac, R = 0.2007 (Rfree = 0.000) for 7409 atoms. Found 8 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 7635 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 7652 seeds are put forward Round 1: 441 peptides, 80 chains. Longest chain 11 peptides. Score 0.359 Round 2: 501 peptides, 80 chains. Longest chain 18 peptides. Score 0.441 Round 3: 506 peptides, 77 chains. Longest chain 22 peptides. Score 0.465 Round 4: 491 peptides, 77 chains. Longest chain 15 peptides. Score 0.445 Round 5: 493 peptides, 78 chains. Longest chain 21 peptides. Score 0.442 Taking the results from Round 3 Chains 77, Residues 429, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17427 restraints for refining 7506 atoms. 15769 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2300 (Rfree = 0.000) for 7506 atoms. Found 48 (48 requested) and removed 37 (24 requested) atoms. Cycle 27: After refmac, R = 0.2212 (Rfree = 0.000) for 7499 atoms. Found 13 (48 requested) and removed 24 (24 requested) atoms. Cycle 28: After refmac, R = 0.2187 (Rfree = 0.000) for 7481 atoms. Found 11 (48 requested) and removed 24 (24 requested) atoms. Cycle 29: After refmac, R = 0.2178 (Rfree = 0.000) for 7465 atoms. Found 5 (47 requested) and removed 23 (23 requested) atoms. Cycle 30: After refmac, R = 0.2193 (Rfree = 0.000) for 7445 atoms. Found 3 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 7611 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 7634 seeds are put forward Round 1: 414 peptides, 81 chains. Longest chain 11 peptides. Score 0.312 Round 2: 489 peptides, 82 chains. Longest chain 16 peptides. Score 0.414 Round 3: 490 peptides, 77 chains. Longest chain 13 peptides. Score 0.444 Round 4: 477 peptides, 77 chains. Longest chain 16 peptides. Score 0.427 Round 5: 487 peptides, 78 chains. Longest chain 14 peptides. Score 0.434 Taking the results from Round 3 Chains 77, Residues 413, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17409 restraints for refining 7505 atoms. 15761 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2298 (Rfree = 0.000) for 7505 atoms. Found 23 (48 requested) and removed 31 (24 requested) atoms. Cycle 32: After refmac, R = 0.2127 (Rfree = 0.000) for 7473 atoms. Found 13 (48 requested) and removed 25 (24 requested) atoms. Cycle 33: After refmac, R = 0.2075 (Rfree = 0.000) for 7455 atoms. Found 7 (47 requested) and removed 26 (23 requested) atoms. Cycle 34: After refmac, R = 0.2095 (Rfree = 0.000) for 7433 atoms. Found 7 (47 requested) and removed 25 (23 requested) atoms. Cycle 35: After refmac, R = 0.2082 (Rfree = 0.000) for 7413 atoms. Found 6 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 7614 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7630 seeds are put forward Round 1: 383 peptides, 78 chains. Longest chain 10 peptides. Score 0.284 Round 2: 444 peptides, 74 chains. Longest chain 14 peptides. Score 0.400 Round 3: 440 peptides, 74 chains. Longest chain 13 peptides. Score 0.394 Round 4: 441 peptides, 70 chains. Longest chain 15 peptides. Score 0.420 Round 5: 436 peptides, 71 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 4 Chains 70, Residues 371, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17791 restraints for refining 7504 atoms. 16327 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2241 (Rfree = 0.000) for 7504 atoms. Found 37 (48 requested) and removed 30 (24 requested) atoms. Cycle 37: After refmac, R = 0.2128 (Rfree = 0.000) for 7482 atoms. Found 12 (48 requested) and removed 25 (24 requested) atoms. Cycle 38: After refmac, R = 0.2105 (Rfree = 0.000) for 7465 atoms. Found 8 (47 requested) and removed 23 (23 requested) atoms. Cycle 39: After refmac, R = 0.2087 (Rfree = 0.000) for 7449 atoms. Found 3 (47 requested) and removed 23 (23 requested) atoms. Cycle 40: After refmac, R = 0.2090 (Rfree = 0.000) for 7429 atoms. Found 5 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 7589 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7609 seeds are put forward Round 1: 371 peptides, 74 chains. Longest chain 11 peptides. Score 0.292 Round 2: 424 peptides, 70 chains. Longest chain 12 peptides. Score 0.396 Round 3: 412 peptides, 74 chains. Longest chain 13 peptides. Score 0.354 Round 4: 430 peptides, 68 chains. Longest chain 14 peptides. Score 0.417 Round 5: 444 peptides, 70 chains. Longest chain 17 peptides. Score 0.424 Taking the results from Round 5 Chains 70, Residues 374, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17771 restraints for refining 7506 atoms. 16303 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2256 (Rfree = 0.000) for 7506 atoms. Found 41 (48 requested) and removed 29 (24 requested) atoms. Cycle 42: After refmac, R = 0.2096 (Rfree = 0.000) for 7500 atoms. Found 10 (48 requested) and removed 25 (24 requested) atoms. Cycle 43: After refmac, R = 0.2046 (Rfree = 0.000) for 7477 atoms. Found 8 (48 requested) and removed 24 (24 requested) atoms. Cycle 44: After refmac, R = 0.2029 (Rfree = 0.000) for 7458 atoms. Found 6 (47 requested) and removed 23 (23 requested) atoms. Cycle 45: After refmac, R = 0.2008 (Rfree = 0.000) for 7437 atoms. Found 6 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 7602 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 7632 seeds are put forward Round 1: 368 peptides, 71 chains. Longest chain 13 peptides. Score 0.307 Round 2: 412 peptides, 72 chains. Longest chain 17 peptides. Score 0.366 Round 3: 435 peptides, 74 chains. Longest chain 14 peptides. Score 0.387 Round 4: 433 peptides, 68 chains. Longest chain 15 peptides. Score 0.421 Round 5: 405 peptides, 69 chains. Longest chain 14 peptides. Score 0.375 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 68, Residues 365, Estimated correctness of the model 0.0 % 2 chains (12 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 68 chains (365 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14118 reflections ( 99.56 % complete ) and 17834 restraints for refining 7506 atoms. 16411 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2177 (Rfree = 0.000) for 7506 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2063 (Rfree = 0.000) for 7448 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.2073 (Rfree = 0.000) for 7409 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.2054 (Rfree = 0.000) for 7376 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:53:02 GMT 2018 Job finished. TimeTaking 90.27 Used memory is bytes: 5646384