Mon 24 Dec 00:41:27 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 1vl4-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-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/1vl4-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-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 00:41:31 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/1vl4-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-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 719 and 0 Target number of residues in the AU: 719 Target solvent content: 0.6219 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-3.6-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7152 target number of atoms Had to go as low as 0.65 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: 79.862 3.600 Wilson plot Bfac: 62.30 12391 reflections ( 99.37 % complete ) and 0 restraints for refining 7899 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3089 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3050 (Rfree = 0.000) for 7899 atoms. Found 50 (50 requested) and removed 44 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 8003 seeds are put forward NCS extension: 0 residues added, 8003 seeds are put forward Round 1: 362 peptides, 62 chains. Longest chain 14 peptides. Score 0.375 Round 2: 502 peptides, 65 chains. Longest chain 23 peptides. Score 0.558 Round 3: 559 peptides, 71 chains. Longest chain 32 peptides. Score 0.595 Round 4: 552 peptides, 69 chains. Longest chain 25 peptides. Score 0.597 Round 5: 567 peptides, 63 chains. Longest chain 31 peptides. Score 0.644 Taking the results from Round 5 Chains 71, Residues 504, Estimated correctness of the model 31.0 % 10 chains (99 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 13305 restraints for refining 6457 atoms. 11008 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2543 (Rfree = 0.000) for 6457 atoms. Found 36 (41 requested) and removed 66 (20 requested) atoms. Cycle 2: After refmac, R = 0.2363 (Rfree = 0.000) for 6316 atoms. Found 24 (41 requested) and removed 48 (20 requested) atoms. Cycle 3: After refmac, R = 0.2306 (Rfree = 0.000) for 6267 atoms. Found 12 (40 requested) and removed 53 (20 requested) atoms. Cycle 4: After refmac, R = 0.2271 (Rfree = 0.000) for 6214 atoms. Found 24 (39 requested) and removed 42 (19 requested) atoms. Cycle 5: After refmac, R = 0.2246 (Rfree = 0.000) for 6188 atoms. Found 24 (39 requested) and removed 37 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6393 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 6409 seeds are put forward Round 1: 509 peptides, 75 chains. Longest chain 19 peptides. Score 0.509 Round 2: 535 peptides, 66 chains. Longest chain 24 peptides. Score 0.593 Round 3: 537 peptides, 62 chains. Longest chain 29 peptides. Score 0.616 Round 4: 534 peptides, 60 chains. Longest chain 28 peptides. Score 0.623 Round 5: 539 peptides, 60 chains. Longest chain 33 peptides. Score 0.629 Taking the results from Round 5 Chains 63, Residues 479, Estimated correctness of the model 25.6 % 6 chains (70 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 13910 restraints for refining 6483 atoms. 11799 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2570 (Rfree = 0.000) for 6483 atoms. Found 41 (41 requested) and removed 51 (20 requested) atoms. Cycle 7: After refmac, R = 0.2502 (Rfree = 0.000) for 6432 atoms. Found 33 (41 requested) and removed 45 (20 requested) atoms. Cycle 8: After refmac, R = 0.2178 (Rfree = 0.000) for 6399 atoms. Found 11 (41 requested) and removed 30 (20 requested) atoms. Cycle 9: After refmac, R = 0.2279 (Rfree = 0.000) for 6359 atoms. Found 28 (40 requested) and removed 31 (20 requested) atoms. Cycle 10: After refmac, R = 0.2391 (Rfree = 0.000) for 6348 atoms. Found 40 (40 requested) and removed 41 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.21 Search for helices and strands: 0 residues in 0 chains, 6541 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6560 seeds are put forward Round 1: 481 peptides, 77 chains. Longest chain 21 peptides. Score 0.458 Round 2: 522 peptides, 73 chains. Longest chain 24 peptides. Score 0.538 Round 3: 531 peptides, 69 chains. Longest chain 22 peptides. Score 0.572 Round 4: 555 peptides, 69 chains. Longest chain 24 peptides. Score 0.600 Round 5: 542 peptides, 69 chains. Longest chain 22 peptides. Score 0.585 Taking the results from Round 4 Chains 77, Residues 486, Estimated correctness of the model 14.7 % 9 chains (90 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 13603 restraints for refining 6482 atoms. 11401 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2499 (Rfree = 0.000) for 6482 atoms. Found 27 (41 requested) and removed 57 (20 requested) atoms. Cycle 12: After refmac, R = 0.2361 (Rfree = 0.000) for 6409 atoms. Found 25 (41 requested) and removed 42 (20 requested) atoms. Cycle 13: After refmac, R = 0.2240 (Rfree = 0.000) for 6384 atoms. Found 14 (41 requested) and removed 28 (20 requested) atoms. Cycle 14: After refmac, R = 0.2172 (Rfree = 0.000) for 6358 atoms. Found 16 (40 requested) and removed 36 (20 requested) atoms. Cycle 15: After refmac, R = 0.2097 (Rfree = 0.000) for 6328 atoms. Found 15 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.22 Search for helices and strands: 0 residues in 0 chains, 6527 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 6550 seeds are put forward Round 1: 463 peptides, 74 chains. Longest chain 23 peptides. Score 0.450 Round 2: 501 peptides, 69 chains. Longest chain 24 peptides. Score 0.534 Round 3: 516 peptides, 70 chains. Longest chain 24 peptides. Score 0.547 Round 4: 518 peptides, 64 chains. Longest chain 24 peptides. Score 0.583 Round 5: 501 peptides, 64 chains. Longest chain 24 peptides. Score 0.562 Taking the results from Round 4 Chains 65, Residues 454, Estimated correctness of the model 7.9 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14037 restraints for refining 6480 atoms. 12061 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2392 (Rfree = 0.000) for 6480 atoms. Found 29 (41 requested) and removed 50 (20 requested) atoms. Cycle 17: After refmac, R = 0.2281 (Rfree = 0.000) for 6422 atoms. Found 23 (41 requested) and removed 26 (20 requested) atoms. Cycle 18: After refmac, R = 0.2250 (Rfree = 0.000) for 6381 atoms. Found 30 (41 requested) and removed 26 (20 requested) atoms. Cycle 19: After refmac, R = 0.2206 (Rfree = 0.000) for 6354 atoms. Found 37 (40 requested) and removed 26 (20 requested) atoms. Cycle 20: After refmac, R = 0.1972 (Rfree = 0.000) for 6333 atoms. Found 12 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.20 Search for helices and strands: 0 residues in 0 chains, 6484 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 6514 seeds are put forward Round 1: 438 peptides, 72 chains. Longest chain 18 peptides. Score 0.426 Round 2: 518 peptides, 70 chains. Longest chain 25 peptides. Score 0.550 Round 3: 493 peptides, 67 chains. Longest chain 23 peptides. Score 0.535 Round 4: 488 peptides, 64 chains. Longest chain 31 peptides. Score 0.546 Round 5: 520 peptides, 69 chains. Longest chain 16 peptides. Score 0.558 Taking the results from Round 5 Chains 69, Residues 451, Estimated correctness of the model 0.0 % 7 chains (63 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 13834 restraints for refining 6482 atoms. 11859 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2258 (Rfree = 0.000) for 6482 atoms. Found 25 (41 requested) and removed 43 (20 requested) atoms. Cycle 22: After refmac, R = 0.2261 (Rfree = 0.000) for 6437 atoms. Found 29 (41 requested) and removed 26 (20 requested) atoms. Cycle 23: After refmac, R = 0.2235 (Rfree = 0.000) for 6415 atoms. Found 28 (41 requested) and removed 34 (20 requested) atoms. Cycle 24: After refmac, R = 0.2070 (Rfree = 0.000) for 6385 atoms. Found 12 (41 requested) and removed 28 (20 requested) atoms. Cycle 25: After refmac, R = 0.2064 (Rfree = 0.000) for 6358 atoms. Found 5 (40 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.17 Search for helices and strands: 0 residues in 0 chains, 6488 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6504 seeds are put forward Round 1: 432 peptides, 73 chains. Longest chain 16 peptides. Score 0.410 Round 2: 467 peptides, 64 chains. Longest chain 21 peptides. Score 0.518 Round 3: 483 peptides, 65 chains. Longest chain 18 peptides. Score 0.534 Round 4: 484 peptides, 63 chains. Longest chain 23 peptides. Score 0.547 Round 5: 488 peptides, 66 chains. Longest chain 27 peptides. Score 0.534 Taking the results from Round 4 Chains 63, Residues 421, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14265 restraints for refining 6483 atoms. 12491 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2433 (Rfree = 0.000) for 6483 atoms. Found 41 (41 requested) and removed 43 (20 requested) atoms. Cycle 27: After refmac, R = 0.2371 (Rfree = 0.000) for 6436 atoms. Found 41 (41 requested) and removed 32 (20 requested) atoms. Cycle 28: After refmac, R = 0.2028 (Rfree = 0.000) for 6415 atoms. Found 20 (41 requested) and removed 30 (20 requested) atoms. Cycle 29: After refmac, R = 0.2028 (Rfree = 0.000) for 6377 atoms. Found 7 (41 requested) and removed 25 (20 requested) atoms. Cycle 30: After refmac, R = 0.2027 (Rfree = 0.000) for 6349 atoms. Found 16 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.18 Search for helices and strands: 0 residues in 0 chains, 6471 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6490 seeds are put forward Round 1: 399 peptides, 75 chains. Longest chain 17 peptides. Score 0.344 Round 2: 455 peptides, 72 chains. Longest chain 17 peptides. Score 0.452 Round 3: 457 peptides, 69 chains. Longest chain 22 peptides. Score 0.473 Round 4: 468 peptides, 68 chains. Longest chain 25 peptides. Score 0.495 Round 5: 463 peptides, 67 chains. Longest chain 20 peptides. Score 0.494 Taking the results from Round 4 Chains 69, Residues 400, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14479 restraints for refining 6483 atoms. 12806 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2471 (Rfree = 0.000) for 6483 atoms. Found 41 (41 requested) and removed 50 (20 requested) atoms. Cycle 32: After refmac, R = 0.2189 (Rfree = 0.000) for 6452 atoms. Found 33 (41 requested) and removed 33 (20 requested) atoms. Cycle 33: After refmac, R = 0.2158 (Rfree = 0.000) for 6432 atoms. Found 28 (41 requested) and removed 33 (20 requested) atoms. Cycle 34: After refmac, R = 0.2018 (Rfree = 0.000) for 6421 atoms. Found 21 (41 requested) and removed 22 (20 requested) atoms. Cycle 35: After refmac, R = 0.2065 (Rfree = 0.000) for 6412 atoms. Found 22 (41 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.18 Search for helices and strands: 0 residues in 0 chains, 6582 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6599 seeds are put forward Round 1: 392 peptides, 76 chains. Longest chain 11 peptides. Score 0.325 Round 2: 433 peptides, 72 chains. Longest chain 13 peptides. Score 0.419 Round 3: 417 peptides, 66 chains. Longest chain 15 peptides. Score 0.434 Round 4: 420 peptides, 66 chains. Longest chain 14 peptides. Score 0.439 Round 5: 436 peptides, 70 chains. Longest chain 15 peptides. Score 0.436 Taking the results from Round 4 Chains 66, Residues 354, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14990 restraints for refining 6483 atoms. 13599 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2359 (Rfree = 0.000) for 6483 atoms. Found 32 (41 requested) and removed 34 (20 requested) atoms. Cycle 37: After refmac, R = 0.2382 (Rfree = 0.000) for 6437 atoms. Found 41 (41 requested) and removed 41 (20 requested) atoms. Cycle 38: After refmac, R = 0.2326 (Rfree = 0.000) for 6402 atoms. Found 41 (41 requested) and removed 36 (20 requested) atoms. Cycle 39: After refmac, R = 0.2229 (Rfree = 0.000) for 6384 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. Cycle 40: After refmac, R = 0.2206 (Rfree = 0.000) for 6366 atoms. Found 41 (41 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6517 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6533 seeds are put forward Round 1: 344 peptides, 68 chains. Longest chain 9 peptides. Score 0.301 Round 2: 418 peptides, 70 chains. Longest chain 13 peptides. Score 0.409 Round 3: 425 peptides, 69 chains. Longest chain 13 peptides. Score 0.426 Round 4: 421 peptides, 66 chains. Longest chain 15 peptides. Score 0.440 Round 5: 426 peptides, 64 chains. Longest chain 15 peptides. Score 0.460 Taking the results from Round 5 Chains 67, Residues 362, Estimated correctness of the model 0.0 % 6 chains (52 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14294 restraints for refining 6482 atoms. 12726 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2502 (Rfree = 0.000) for 6482 atoms. Found 41 (41 requested) and removed 36 (20 requested) atoms. Cycle 42: After refmac, R = 0.2417 (Rfree = 0.000) for 6447 atoms. Found 41 (41 requested) and removed 38 (20 requested) atoms. Cycle 43: After refmac, R = 0.2373 (Rfree = 0.000) for 6430 atoms. Found 41 (41 requested) and removed 28 (20 requested) atoms. Cycle 44: After refmac, R = 0.2108 (Rfree = 0.000) for 6421 atoms. Found 21 (41 requested) and removed 27 (20 requested) atoms. Cycle 45: After refmac, R = 0.2038 (Rfree = 0.000) for 6405 atoms. Found 9 (41 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 6545 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6565 seeds are put forward Round 1: 318 peptides, 63 chains. Longest chain 10 peptides. Score 0.293 Round 2: 366 peptides, 61 chains. Longest chain 13 peptides. Score 0.389 Round 3: 363 peptides, 62 chains. Longest chain 11 peptides. Score 0.377 Round 4: 375 peptides, 58 chains. Longest chain 16 peptides. Score 0.424 Round 5: 388 peptides, 61 chains. Longest chain 15 peptides. Score 0.423 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 317, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 59 chains (317 residues) following loop building 3 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12391 reflections ( 99.37 % complete ) and 15006 restraints for refining 6482 atoms. 13718 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2371 (Rfree = 0.000) for 6482 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2327 (Rfree = 0.000) for 6442 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2151 (Rfree = 0.000) for 6402 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.2212 (Rfree = 0.000) for 6366 atoms. TimeTaking 63.68