null Mon 24 Dec 00:03:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vqr-3.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:04:01 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-parrot-mrncs/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 1001 and 0 Target number of residues in the AU: 1001 Target solvent content: 0.5680 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-3.0-parrot-mrncs.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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9504 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: 83.418 3.000 Wilson plot Bfac: 40.94 21657 reflections ( 87.44 % complete ) and 0 restraints for refining 10466 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3605 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3140 (Rfree = 0.000) for 10466 atoms. Found 83 (112 requested) and removed 166 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.74 2.78 Search for helices and strands: 0 residues in 0 chains, 10547 seeds are put forward NCS extension: 0 residues added, 10547 seeds are put forward Round 1: 346 peptides, 78 chains. Longest chain 8 peptides. Score 0.222 Round 2: 431 peptides, 88 chains. Longest chain 12 peptides. Score 0.287 Round 3: 462 peptides, 93 chains. Longest chain 12 peptides. Score 0.301 Round 4: 469 peptides, 87 chains. Longest chain 16 peptides. Score 0.346 Round 5: 441 peptides, 79 chains. Longest chain 16 peptides. Score 0.355 Taking the results from Round 5 Chains 79, Residues 362, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 20084 restraints for refining 8719 atoms. 18670 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2698 (Rfree = 0.000) for 8719 atoms. Found 50 (94 requested) and removed 62 (47 requested) atoms. Cycle 2: After refmac, R = 0.2581 (Rfree = 0.000) for 8645 atoms. Found 33 (93 requested) and removed 52 (46 requested) atoms. Cycle 3: After refmac, R = 0.2500 (Rfree = 0.000) for 8588 atoms. Found 31 (93 requested) and removed 52 (46 requested) atoms. Cycle 4: After refmac, R = 0.2447 (Rfree = 0.000) for 8549 atoms. Found 23 (92 requested) and removed 46 (46 requested) atoms. Cycle 5: After refmac, R = 0.2422 (Rfree = 0.000) for 8516 atoms. Found 20 (91 requested) and removed 48 (45 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.69 2.73 Search for helices and strands: 0 residues in 0 chains, 8753 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8768 seeds are put forward Round 1: 443 peptides, 90 chains. Longest chain 13 peptides. Score 0.292 Round 2: 483 peptides, 90 chains. Longest chain 12 peptides. Score 0.348 Round 3: 474 peptides, 90 chains. Longest chain 12 peptides. Score 0.335 Round 4: 487 peptides, 87 chains. Longest chain 14 peptides. Score 0.370 Round 5: 488 peptides, 88 chains. Longest chain 12 peptides. Score 0.366 Taking the results from Round 4 Chains 87, Residues 400, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19689 restraints for refining 8546 atoms. 18176 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2475 (Rfree = 0.000) for 8546 atoms. Found 46 (92 requested) and removed 58 (46 requested) atoms. Cycle 7: After refmac, R = 0.2374 (Rfree = 0.000) for 8504 atoms. Found 19 (92 requested) and removed 53 (46 requested) atoms. Cycle 8: After refmac, R = 0.2367 (Rfree = 0.000) for 8446 atoms. Found 17 (91 requested) and removed 51 (45 requested) atoms. Cycle 9: After refmac, R = 0.2306 (Rfree = 0.000) for 8398 atoms. Found 12 (90 requested) and removed 51 (45 requested) atoms. Cycle 10: After refmac, R = 0.2310 (Rfree = 0.000) for 8347 atoms. Found 25 (90 requested) and removed 47 (45 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.70 2.74 Search for helices and strands: 0 residues in 0 chains, 8603 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 8618 seeds are put forward Round 1: 464 peptides, 96 chains. Longest chain 14 peptides. Score 0.286 Round 2: 468 peptides, 85 chains. Longest chain 18 peptides. Score 0.356 Round 3: 484 peptides, 83 chains. Longest chain 18 peptides. Score 0.389 Round 4: 495 peptides, 85 chains. Longest chain 18 peptides. Score 0.392 Round 5: 484 peptides, 80 chains. Longest chain 21 peptides. Score 0.406 Taking the results from Round 5 Chains 80, Residues 404, Estimated correctness of the model 0.8 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19374 restraints for refining 8528 atoms. 17790 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2456 (Rfree = 0.000) for 8528 atoms. Found 55 (92 requested) and removed 68 (46 requested) atoms. Cycle 12: After refmac, R = 0.2336 (Rfree = 0.000) for 8494 atoms. Found 20 (91 requested) and removed 54 (45 requested) atoms. Cycle 13: After refmac, R = 0.2276 (Rfree = 0.000) for 8443 atoms. Found 15 (91 requested) and removed 49 (45 requested) atoms. Cycle 14: After refmac, R = 0.2272 (Rfree = 0.000) for 8397 atoms. Found 11 (90 requested) and removed 49 (45 requested) atoms. Cycle 15: After refmac, R = 0.2242 (Rfree = 0.000) for 8351 atoms. Found 17 (90 requested) and removed 50 (45 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.74 2.78 Search for helices and strands: 0 residues in 0 chains, 8549 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 8576 seeds are put forward Round 1: 448 peptides, 90 chains. Longest chain 13 peptides. Score 0.299 Round 2: 476 peptides, 84 chains. Longest chain 24 peptides. Score 0.373 Round 3: 478 peptides, 83 chains. Longest chain 20 peptides. Score 0.381 Round 4: 483 peptides, 83 chains. Longest chain 13 peptides. Score 0.388 Round 5: 461 peptides, 79 chains. Longest chain 12 peptides. Score 0.382 Taking the results from Round 4 Chains 83, Residues 400, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19671 restraints for refining 8568 atoms. 18138 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2297 (Rfree = 0.000) for 8568 atoms. Found 33 (92 requested) and removed 49 (46 requested) atoms. Cycle 17: After refmac, R = 0.2231 (Rfree = 0.000) for 8541 atoms. Found 22 (92 requested) and removed 50 (46 requested) atoms. Cycle 18: After refmac, R = 0.2182 (Rfree = 0.000) for 8505 atoms. Found 22 (91 requested) and removed 46 (45 requested) atoms. Cycle 19: After refmac, R = 0.2159 (Rfree = 0.000) for 8474 atoms. Found 7 (91 requested) and removed 45 (45 requested) atoms. Cycle 20: After refmac, R = 0.2153 (Rfree = 0.000) for 8431 atoms. Found 15 (90 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.74 2.78 Search for helices and strands: 0 residues in 0 chains, 8657 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8671 seeds are put forward Round 1: 458 peptides, 91 chains. Longest chain 10 peptides. Score 0.307 Round 2: 496 peptides, 87 chains. Longest chain 15 peptides. Score 0.382 Round 3: 493 peptides, 84 chains. Longest chain 21 peptides. Score 0.395 Round 4: 495 peptides, 86 chains. Longest chain 13 peptides. Score 0.386 Round 5: 519 peptides, 89 chains. Longest chain 13 peptides. Score 0.401 Taking the results from Round 5 Chains 89, Residues 430, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19904 restraints for refining 8706 atoms. 18273 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2383 (Rfree = 0.000) for 8706 atoms. Found 48 (93 requested) and removed 57 (46 requested) atoms. Cycle 22: After refmac, R = 0.2244 (Rfree = 0.000) for 8685 atoms. Found 33 (93 requested) and removed 51 (46 requested) atoms. Cycle 23: After refmac, R = 0.2257 (Rfree = 0.000) for 8655 atoms. Found 15 (93 requested) and removed 46 (46 requested) atoms. Cycle 24: After refmac, R = 0.2191 (Rfree = 0.000) for 8619 atoms. Found 12 (93 requested) and removed 46 (46 requested) atoms. Cycle 25: After refmac, R = 0.2202 (Rfree = 0.000) for 8584 atoms. Found 13 (92 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.74 2.78 Search for helices and strands: 0 residues in 0 chains, 8814 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8829 seeds are put forward Round 1: 417 peptides, 85 chains. Longest chain 10 peptides. Score 0.285 Round 2: 469 peptides, 81 chains. Longest chain 14 peptides. Score 0.381 Round 3: 488 peptides, 80 chains. Longest chain 16 peptides. Score 0.411 Round 4: 490 peptides, 83 chains. Longest chain 15 peptides. Score 0.397 Round 5: 492 peptides, 80 chains. Longest chain 19 peptides. Score 0.416 Taking the results from Round 5 Chains 80, Residues 412, Estimated correctness of the model 3.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 20140 restraints for refining 8722 atoms. 18572 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2288 (Rfree = 0.000) for 8722 atoms. Found 40 (94 requested) and removed 48 (47 requested) atoms. Cycle 27: After refmac, R = 0.2188 (Rfree = 0.000) for 8705 atoms. Found 22 (93 requested) and removed 46 (46 requested) atoms. Cycle 28: After refmac, R = 0.2162 (Rfree = 0.000) for 8676 atoms. Found 23 (93 requested) and removed 46 (46 requested) atoms. Cycle 29: After refmac, R = 0.2097 (Rfree = 0.000) for 8644 atoms. Found 19 (93 requested) and removed 46 (46 requested) atoms. Cycle 30: After refmac, R = 0.2093 (Rfree = 0.000) for 8612 atoms. Found 15 (92 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.73 2.77 Search for helices and strands: 0 residues in 0 chains, 8809 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8824 seeds are put forward Round 1: 448 peptides, 93 chains. Longest chain 13 peptides. Score 0.281 Round 2: 484 peptides, 89 chains. Longest chain 22 peptides. Score 0.355 Round 3: 463 peptides, 82 chains. Longest chain 22 peptides. Score 0.367 Round 4: 462 peptides, 79 chains. Longest chain 17 peptides. Score 0.383 Round 5: 472 peptides, 82 chains. Longest chain 18 peptides. Score 0.379 Taking the results from Round 4 Chains 79, Residues 383, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 20071 restraints for refining 8723 atoms. 18618 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2241 (Rfree = 0.000) for 8723 atoms. Found 50 (94 requested) and removed 49 (47 requested) atoms. Cycle 32: After refmac, R = 0.2171 (Rfree = 0.000) for 8711 atoms. Found 24 (94 requested) and removed 50 (47 requested) atoms. Cycle 33: After refmac, R = 0.2168 (Rfree = 0.000) for 8673 atoms. Found 25 (93 requested) and removed 47 (46 requested) atoms. Cycle 34: After refmac, R = 0.2143 (Rfree = 0.000) for 8645 atoms. Found 12 (93 requested) and removed 48 (46 requested) atoms. Cycle 35: After refmac, R = 0.2103 (Rfree = 0.000) for 8607 atoms. Found 14 (92 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.72 2.76 Search for helices and strands: 0 residues in 0 chains, 8799 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 8824 seeds are put forward Round 1: 405 peptides, 83 chains. Longest chain 12 peptides. Score 0.280 Round 2: 485 peptides, 85 chains. Longest chain 16 peptides. Score 0.379 Round 3: 475 peptides, 86 chains. Longest chain 12 peptides. Score 0.360 Round 4: 457 peptides, 82 chains. Longest chain 17 peptides. Score 0.359 Round 5: 458 peptides, 85 chains. Longest chain 17 peptides. Score 0.343 Taking the results from Round 2 Chains 85, Residues 400, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19579 restraints for refining 8702 atoms. 18049 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2172 (Rfree = 0.000) for 8702 atoms. Found 36 (93 requested) and removed 50 (46 requested) atoms. Cycle 37: After refmac, R = 0.2131 (Rfree = 0.000) for 8671 atoms. Found 15 (93 requested) and removed 47 (46 requested) atoms. Cycle 38: After refmac, R = 0.2093 (Rfree = 0.000) for 8630 atoms. Found 18 (93 requested) and removed 46 (46 requested) atoms. Cycle 39: After refmac, R = 0.2035 (Rfree = 0.000) for 8590 atoms. Found 13 (92 requested) and removed 48 (46 requested) atoms. Cycle 40: After refmac, R = 0.1998 (Rfree = 0.000) for 8550 atoms. Found 7 (92 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.73 2.77 Search for helices and strands: 0 residues in 0 chains, 8725 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 8749 seeds are put forward Round 1: 362 peptides, 75 chains. Longest chain 12 peptides. Score 0.266 Round 2: 428 peptides, 77 chains. Longest chain 15 peptides. Score 0.349 Round 3: 430 peptides, 74 chains. Longest chain 15 peptides. Score 0.369 Round 4: 413 peptides, 74 chains. Longest chain 15 peptides. Score 0.346 Round 5: 417 peptides, 76 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 3 Chains 74, Residues 356, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19586 restraints for refining 8606 atoms. 18210 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2129 (Rfree = 0.000) for 8606 atoms. Found 38 (92 requested) and removed 47 (46 requested) atoms. Cycle 42: After refmac, R = 0.2034 (Rfree = 0.000) for 8591 atoms. Found 19 (92 requested) and removed 46 (46 requested) atoms. Cycle 43: After refmac, R = 0.2009 (Rfree = 0.000) for 8560 atoms. Found 13 (92 requested) and removed 46 (46 requested) atoms. Cycle 44: After refmac, R = 0.1974 (Rfree = 0.000) for 8518 atoms. Found 10 (91 requested) and removed 45 (45 requested) atoms. Cycle 45: After refmac, R = 0.1984 (Rfree = 0.000) for 8476 atoms. Found 14 (91 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.76 2.80 Search for helices and strands: 0 residues in 0 chains, 8662 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 8677 seeds are put forward Round 1: 358 peptides, 70 chains. Longest chain 11 peptides. Score 0.292 Round 2: 381 peptides, 67 chains. Longest chain 15 peptides. Score 0.344 Round 3: 398 peptides, 68 chains. Longest chain 19 peptides. Score 0.361 Round 4: 407 peptides, 74 chains. Longest chain 13 peptides. Score 0.338 Round 5: 383 peptides, 70 chains. Longest chain 14 peptides. Score 0.328 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 68, Residues 330, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 1vqr-3_warpNtrace.pdb as input Building loops using Loopy2018 68 chains (330 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21657 reflections ( 87.44 % complete ) and 19324 restraints for refining 8497 atoms. 18054 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2037 (Rfree = 0.000) for 8497 atoms. Found 0 (91 requested) and removed 45 (45 requested) atoms. Cycle 47: After refmac, R = 0.2020 (Rfree = 0.000) for 8443 atoms. Found 0 (91 requested) and removed 18 (45 requested) atoms. Cycle 48: After refmac, R = 0.2010 (Rfree = 0.000) for 8423 atoms. Found 0 (90 requested) and removed 12 (45 requested) atoms. Cycle 49: After refmac, R = 0.2016 (Rfree = 0.000) for 8408 atoms. Found 0 (90 requested) and removed 25 (45 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:30:09 GMT 2018 Job finished. TimeTaking 86.19 Used memory is bytes: 16676728