null Sun 23 Dec 23:48:00 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.2-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-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.2-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 ============================================================ Sun 23 Dec 23:48:05 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.2-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 967 and 0 Target number of residues in the AU: 967 Target solvent content: 0.5827 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-3.2-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-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.75 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 3.200 Wilson plot Bfac: 45.87 18027 reflections ( 88.16 % complete ) and 0 restraints for refining 10518 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3556 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3137 (Rfree = 0.000) for 10518 atoms. Found 76 (94 requested) and removed 170 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.06 3.10 Search for helices and strands: 0 residues in 0 chains, 10617 seeds are put forward NCS extension: 0 residues added, 10617 seeds are put forward Round 1: 329 peptides, 73 chains. Longest chain 8 peptides. Score 0.228 Round 2: 430 peptides, 88 chains. Longest chain 9 peptides. Score 0.286 Round 3: 469 peptides, 94 chains. Longest chain 9 peptides. Score 0.305 Round 4: 484 peptides, 93 chains. Longest chain 10 peptides. Score 0.332 Round 5: 500 peptides, 93 chains. Longest chain 12 peptides. Score 0.353 Taking the results from Round 5 Chains 93, Residues 407, Estimated correctness of the model 0.0 % 5 chains (19 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20148 restraints for refining 8675 atoms. 18555 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2777 (Rfree = 0.000) for 8675 atoms. Found 54 (77 requested) and removed 53 (38 requested) atoms. Cycle 2: After refmac, R = 0.2707 (Rfree = 0.000) for 8595 atoms. Found 41 (77 requested) and removed 57 (38 requested) atoms. Cycle 3: After refmac, R = 0.2359 (Rfree = 0.000) for 8531 atoms. Found 17 (76 requested) and removed 46 (38 requested) atoms. Cycle 4: After refmac, R = 0.2307 (Rfree = 0.000) for 8480 atoms. Found 16 (76 requested) and removed 45 (38 requested) atoms. Cycle 5: After refmac, R = 0.2289 (Rfree = 0.000) for 8431 atoms. Found 9 (75 requested) and removed 43 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.96 3.00 Search for helices and strands: 0 residues in 0 chains, 8676 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8691 seeds are put forward Round 1: 417 peptides, 88 chains. Longest chain 10 peptides. Score 0.267 Round 2: 523 peptides, 97 chains. Longest chain 15 peptides. Score 0.361 Round 3: 513 peptides, 95 chains. Longest chain 18 peptides. Score 0.359 Round 4: 510 peptides, 89 chains. Longest chain 19 peptides. Score 0.389 Round 5: 491 peptides, 89 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 4 Chains 89, Residues 421, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 19594 restraints for refining 8467 atoms. 17969 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2530 (Rfree = 0.000) for 8467 atoms. Found 52 (75 requested) and removed 53 (37 requested) atoms. Cycle 7: After refmac, R = 0.2501 (Rfree = 0.000) for 8437 atoms. Found 54 (75 requested) and removed 49 (37 requested) atoms. Cycle 8: After refmac, R = 0.2538 (Rfree = 0.000) for 8422 atoms. Found 62 (75 requested) and removed 50 (37 requested) atoms. Cycle 9: After refmac, R = 0.2457 (Rfree = 0.000) for 8413 atoms. Found 52 (75 requested) and removed 45 (37 requested) atoms. Cycle 10: After refmac, R = 0.2169 (Rfree = 0.000) for 8403 atoms. Found 12 (75 requested) and removed 45 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.92 2.96 Search for helices and strands: 0 residues in 0 chains, 8641 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 8664 seeds are put forward Round 1: 437 peptides, 87 chains. Longest chain 13 peptides. Score 0.302 Round 2: 490 peptides, 85 chains. Longest chain 14 peptides. Score 0.386 Round 3: 514 peptides, 89 chains. Longest chain 15 peptides. Score 0.394 Round 4: 486 peptides, 82 chains. Longest chain 13 peptides. Score 0.397 Round 5: 481 peptides, 79 chains. Longest chain 18 peptides. Score 0.408 Taking the results from Round 5 Chains 79, Residues 402, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20647 restraints for refining 8672 atoms. 19118 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2399 (Rfree = 0.000) for 8672 atoms. Found 46 (77 requested) and removed 55 (38 requested) atoms. Cycle 12: After refmac, R = 0.2284 (Rfree = 0.000) for 8647 atoms. Found 15 (77 requested) and removed 44 (38 requested) atoms. Cycle 13: After refmac, R = 0.2268 (Rfree = 0.000) for 8605 atoms. Found 17 (77 requested) and removed 51 (38 requested) atoms. Cycle 14: After refmac, R = 0.2250 (Rfree = 0.000) for 8566 atoms. Found 18 (76 requested) and removed 46 (38 requested) atoms. Cycle 15: After refmac, R = 0.2130 (Rfree = 0.000) for 8531 atoms. Found 10 (76 requested) and removed 43 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 3.02 Search for helices and strands: 0 residues in 0 chains, 8725 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 8752 seeds are put forward Round 1: 468 peptides, 96 chains. Longest chain 9 peptides. Score 0.292 Round 2: 535 peptides, 98 chains. Longest chain 13 peptides. Score 0.372 Round 3: 531 peptides, 90 chains. Longest chain 16 peptides. Score 0.410 Round 4: 547 peptides, 91 chains. Longest chain 16 peptides. Score 0.425 Round 5: 562 peptides, 96 chains. Longest chain 12 peptides. Score 0.417 Taking the results from Round 4 Chains 91, Residues 456, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20035 restraints for refining 8676 atoms. 18271 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2442 (Rfree = 0.000) for 8676 atoms. Found 50 (77 requested) and removed 43 (38 requested) atoms. Cycle 17: After refmac, R = 0.2235 (Rfree = 0.000) for 8673 atoms. Found 15 (77 requested) and removed 43 (38 requested) atoms. Cycle 18: After refmac, R = 0.2177 (Rfree = 0.000) for 8637 atoms. Found 13 (77 requested) and removed 45 (38 requested) atoms. Cycle 19: After refmac, R = 0.2171 (Rfree = 0.000) for 8590 atoms. Found 15 (77 requested) and removed 41 (38 requested) atoms. Cycle 20: After refmac, R = 0.2180 (Rfree = 0.000) for 8557 atoms. Found 11 (76 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 3.07 Search for helices and strands: 0 residues in 0 chains, 8769 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8785 seeds are put forward Round 1: 469 peptides, 93 chains. Longest chain 13 peptides. Score 0.311 Round 2: 510 peptides, 94 chains. Longest chain 12 peptides. Score 0.361 Round 3: 517 peptides, 89 chains. Longest chain 14 peptides. Score 0.398 Round 4: 518 peptides, 84 chains. Longest chain 16 peptides. Score 0.427 Round 5: 535 peptides, 83 chains. Longest chain 16 peptides. Score 0.453 Taking the results from Round 5 Chains 83, Residues 452, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20040 restraints for refining 8676 atoms. 18288 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2372 (Rfree = 0.000) for 8676 atoms. Found 56 (77 requested) and removed 41 (38 requested) atoms. Cycle 22: After refmac, R = 0.2222 (Rfree = 0.000) for 8681 atoms. Found 22 (77 requested) and removed 41 (38 requested) atoms. Cycle 23: After refmac, R = 0.2215 (Rfree = 0.000) for 8647 atoms. Found 21 (77 requested) and removed 39 (38 requested) atoms. Cycle 24: After refmac, R = 0.2169 (Rfree = 0.000) for 8624 atoms. Found 15 (77 requested) and removed 39 (38 requested) atoms. Cycle 25: After refmac, R = 0.2150 (Rfree = 0.000) for 8586 atoms. Found 15 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 3.06 Search for helices and strands: 0 residues in 0 chains, 8824 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 8841 seeds are put forward Round 1: 477 peptides, 95 chains. Longest chain 11 peptides. Score 0.310 Round 2: 506 peptides, 89 chains. Longest chain 13 peptides. Score 0.384 Round 3: 510 peptides, 89 chains. Longest chain 13 peptides. Score 0.389 Round 4: 504 peptides, 88 chains. Longest chain 15 peptides. Score 0.387 Round 5: 512 peptides, 85 chains. Longest chain 17 peptides. Score 0.414 Taking the results from Round 5 Chains 85, Residues 427, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20211 restraints for refining 8676 atoms. 18556 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2273 (Rfree = 0.000) for 8676 atoms. Found 46 (77 requested) and removed 44 (38 requested) atoms. Cycle 27: After refmac, R = 0.2192 (Rfree = 0.000) for 8668 atoms. Found 18 (77 requested) and removed 41 (38 requested) atoms. Cycle 28: After refmac, R = 0.2182 (Rfree = 0.000) for 8634 atoms. Found 21 (77 requested) and removed 40 (38 requested) atoms. Cycle 29: After refmac, R = 0.2072 (Rfree = 0.000) for 8611 atoms. Found 12 (77 requested) and removed 39 (38 requested) atoms. Cycle 30: After refmac, R = 0.2086 (Rfree = 0.000) for 8580 atoms. Found 15 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 3.04 Search for helices and strands: 0 residues in 0 chains, 8788 seeds are put forward NCS extension: 24 residues added (6 deleted due to clashes), 8812 seeds are put forward Round 1: 461 peptides, 92 chains. Longest chain 15 peptides. Score 0.306 Round 2: 503 peptides, 90 chains. Longest chain 13 peptides. Score 0.374 Round 3: 490 peptides, 87 chains. Longest chain 10 peptides. Score 0.374 Round 4: 482 peptides, 77 chains. Longest chain 19 peptides. Score 0.420 Round 5: 464 peptides, 82 chains. Longest chain 20 peptides. Score 0.368 Taking the results from Round 4 Chains 77, Residues 405, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20288 restraints for refining 8672 atoms. 18745 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2268 (Rfree = 0.000) for 8672 atoms. Found 44 (77 requested) and removed 39 (38 requested) atoms. Cycle 32: After refmac, R = 0.2162 (Rfree = 0.000) for 8672 atoms. Found 15 (77 requested) and removed 38 (38 requested) atoms. Cycle 33: After refmac, R = 0.2120 (Rfree = 0.000) for 8642 atoms. Found 18 (77 requested) and removed 38 (38 requested) atoms. Cycle 34: After refmac, R = 0.2073 (Rfree = 0.000) for 8619 atoms. Found 11 (77 requested) and removed 38 (38 requested) atoms. Cycle 35: After refmac, R = 0.2041 (Rfree = 0.000) for 8590 atoms. Found 7 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.99 3.03 Search for helices and strands: 0 residues in 0 chains, 8821 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 8844 seeds are put forward Round 1: 396 peptides, 81 chains. Longest chain 11 peptides. Score 0.279 Round 2: 460 peptides, 84 chains. Longest chain 16 peptides. Score 0.351 Round 3: 452 peptides, 78 chains. Longest chain 12 peptides. Score 0.375 Round 4: 440 peptides, 75 chains. Longest chain 15 peptides. Score 0.377 Round 5: 433 peptides, 73 chains. Longest chain 13 peptides. Score 0.379 Taking the results from Round 5 Chains 73, Residues 360, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20546 restraints for refining 8674 atoms. 19159 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2176 (Rfree = 0.000) for 8674 atoms. Found 43 (77 requested) and removed 39 (38 requested) atoms. Cycle 37: After refmac, R = 0.2063 (Rfree = 0.000) for 8666 atoms. Found 18 (77 requested) and removed 39 (38 requested) atoms. Cycle 38: After refmac, R = 0.2022 (Rfree = 0.000) for 8641 atoms. Found 16 (77 requested) and removed 38 (38 requested) atoms. Cycle 39: After refmac, R = 0.1966 (Rfree = 0.000) for 8614 atoms. Found 10 (77 requested) and removed 38 (38 requested) atoms. Cycle 40: After refmac, R = 0.1939 (Rfree = 0.000) for 8585 atoms. Found 4 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.02 3.06 Search for helices and strands: 0 residues in 0 chains, 8776 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 8796 seeds are put forward Round 1: 387 peptides, 83 chains. Longest chain 9 peptides. Score 0.253 Round 2: 422 peptides, 80 chains. Longest chain 12 peptides. Score 0.322 Round 3: 423 peptides, 71 chains. Longest chain 15 peptides. Score 0.377 Round 4: 425 peptides, 77 chains. Longest chain 12 peptides. Score 0.345 Round 5: 440 peptides, 80 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 3 Chains 71, Residues 352, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20442 restraints for refining 8667 atoms. 19105 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2111 (Rfree = 0.000) for 8667 atoms. Found 28 (77 requested) and removed 38 (38 requested) atoms. Cycle 42: After refmac, R = 0.2010 (Rfree = 0.000) for 8650 atoms. Found 6 (77 requested) and removed 41 (38 requested) atoms. Cycle 43: After refmac, R = 0.1970 (Rfree = 0.000) for 8611 atoms. Found 6 (77 requested) and removed 38 (38 requested) atoms. Cycle 44: After refmac, R = 0.1946 (Rfree = 0.000) for 8576 atoms. Found 10 (76 requested) and removed 38 (38 requested) atoms. Cycle 45: After refmac, R = 0.1910 (Rfree = 0.000) for 8548 atoms. Found 4 (76 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 3.09 Search for helices and strands: 0 residues in 0 chains, 8752 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 8762 seeds are put forward Round 1: 390 peptides, 84 chains. Longest chain 9 peptides. Score 0.251 Round 2: 455 peptides, 81 chains. Longest chain 14 peptides. Score 0.362 Round 3: 436 peptides, 80 chains. Longest chain 11 peptides. Score 0.342 Round 4: 445 peptides, 79 chains. Longest chain 12 peptides. Score 0.360 Round 5: 438 peptides, 79 chains. Longest chain 12 peptides. Score 0.351 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 82, Residues 374, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vqr-3_warpNtrace.pdb as input Building loops using Loopy2018 82 chains (374 residues) following loop building 3 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18027 reflections ( 88.16 % complete ) and 19904 restraints for refining 8637 atoms. 18433 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2001 (Rfree = 0.000) for 8637 atoms. Found 0 (77 requested) and removed 26 (38 requested) atoms. Cycle 47: After refmac, R = 0.1975 (Rfree = 0.000) for 8600 atoms. Found 0 (77 requested) and removed 8 (38 requested) atoms. Cycle 48: After refmac, R = 0.1922 (Rfree = 0.000) for 8591 atoms. Found 0 (77 requested) and removed 8 (38 requested) atoms. Cycle 49: After refmac, R = 0.1975 (Rfree = 0.000) for 8578 atoms. Found 0 (77 requested) and removed 8 (38 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:31:18 GMT 2018 Job finished. TimeTaking 103.31 Used memory is bytes: 7445272