null Tue 25 Dec 19:27:57 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 1vl5-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-4.0-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/1vl5-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-4.0-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 ============================================================ Tue 25 Dec 19:28:06 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/1vl5-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-4.0-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 726 and 0 Target number of residues in the AU: 726 Target solvent content: 0.6608 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-4.0-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: 4 Cell parameters: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 8320 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: 49.849 4.000 Wilson plot Bfac: 85.29 9787 reflections ( 99.93 % complete ) and 0 restraints for refining 9219 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3321 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3096 (Rfree = 0.000) for 9219 atoms. Found 43 (43 requested) and removed 38 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 9393 seeds are put forward NCS extension: 0 residues added, 9393 seeds are put forward Round 1: 325 peptides, 66 chains. Longest chain 10 peptides. Score 0.273 Round 2: 475 peptides, 81 chains. Longest chain 14 peptides. Score 0.402 Round 3: 495 peptides, 74 chains. Longest chain 27 peptides. Score 0.469 Round 4: 510 peptides, 77 chains. Longest chain 17 peptides. Score 0.472 Round 5: 528 peptides, 72 chains. Longest chain 20 peptides. Score 0.521 Taking the results from Round 5 Chains 74, Residues 456, Estimated correctness of the model 0.0 % 6 chains (66 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16907 restraints for refining 7513 atoms. 14902 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2475 (Rfree = 0.000) for 7513 atoms. Found 27 (35 requested) and removed 58 (17 requested) atoms. Cycle 2: After refmac, R = 0.2339 (Rfree = 0.000) for 7309 atoms. Found 24 (35 requested) and removed 46 (17 requested) atoms. Cycle 3: After refmac, R = 0.2133 (Rfree = 0.000) for 7195 atoms. Found 16 (34 requested) and removed 49 (17 requested) atoms. Cycle 4: After refmac, R = 0.2096 (Rfree = 0.000) for 7099 atoms. Found 28 (34 requested) and removed 40 (17 requested) atoms. Cycle 5: After refmac, R = 0.1966 (Rfree = 0.000) for 7063 atoms. Found 20 (33 requested) and removed 40 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 7298 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 7323 seeds are put forward Round 1: 463 peptides, 86 chains. Longest chain 14 peptides. Score 0.354 Round 2: 510 peptides, 80 chains. Longest chain 20 peptides. Score 0.455 Round 3: 519 peptides, 75 chains. Longest chain 17 peptides. Score 0.494 Round 4: 536 peptides, 79 chains. Longest chain 15 peptides. Score 0.493 Round 5: 543 peptides, 70 chains. Longest chain 22 peptides. Score 0.549 Taking the results from Round 5 Chains 71, Residues 473, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17083 restraints for refining 7367 atoms. 15237 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2207 (Rfree = 0.000) for 7367 atoms. Found 22 (35 requested) and removed 67 (17 requested) atoms. Cycle 7: After refmac, R = 0.2027 (Rfree = 0.000) for 7236 atoms. Found 22 (34 requested) and removed 53 (17 requested) atoms. Cycle 8: After refmac, R = 0.2039 (Rfree = 0.000) for 7140 atoms. Found 32 (34 requested) and removed 54 (17 requested) atoms. Cycle 9: After refmac, R = 0.2009 (Rfree = 0.000) for 7085 atoms. Found 31 (33 requested) and removed 48 (16 requested) atoms. Cycle 10: After refmac, R = 0.1952 (Rfree = 0.000) for 7047 atoms. Found 33 (33 requested) and removed 47 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 7335 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 7363 seeds are put forward Round 1: 437 peptides, 86 chains. Longest chain 11 peptides. Score 0.316 Round 2: 500 peptides, 74 chains. Longest chain 20 peptides. Score 0.476 Round 3: 490 peptides, 70 chains. Longest chain 21 peptides. Score 0.486 Round 4: 505 peptides, 66 chains. Longest chain 25 peptides. Score 0.526 Round 5: 510 peptides, 67 chains. Longest chain 21 peptides. Score 0.527 Taking the results from Round 5 Chains 67, Residues 443, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17150 restraints for refining 7513 atoms. 15322 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2239 (Rfree = 0.000) for 7513 atoms. Found 31 (35 requested) and removed 85 (17 requested) atoms. Cycle 12: After refmac, R = 0.1987 (Rfree = 0.000) for 7367 atoms. Found 14 (35 requested) and removed 54 (17 requested) atoms. Cycle 13: After refmac, R = 0.1900 (Rfree = 0.000) for 7292 atoms. Found 12 (34 requested) and removed 45 (17 requested) atoms. Cycle 14: After refmac, R = 0.1533 (Rfree = 0.000) for 7210 atoms. Found 11 (34 requested) and removed 35 (17 requested) atoms. Cycle 15: After refmac, R = 0.1461 (Rfree = 0.000) for 7161 atoms. Found 2 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 7411 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 7426 seeds are put forward Round 1: 399 peptides, 74 chains. Longest chain 22 peptides. Score 0.336 Round 2: 453 peptides, 73 chains. Longest chain 14 peptides. Score 0.419 Round 3: 491 peptides, 76 chains. Longest chain 20 peptides. Score 0.453 Round 4: 494 peptides, 68 chains. Longest chain 20 peptides. Score 0.502 Round 5: 483 peptides, 69 chains. Longest chain 22 peptides. Score 0.482 Taking the results from Round 4 Chains 68, Residues 426, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16860 restraints for refining 7413 atoms. 15151 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2103 (Rfree = 0.000) for 7413 atoms. Found 14 (35 requested) and removed 75 (17 requested) atoms. Cycle 17: After refmac, R = 0.1888 (Rfree = 0.000) for 7294 atoms. Found 14 (34 requested) and removed 49 (17 requested) atoms. Cycle 18: After refmac, R = 0.1568 (Rfree = 0.000) for 7216 atoms. Found 5 (34 requested) and removed 34 (17 requested) atoms. Cycle 19: After refmac, R = 0.1463 (Rfree = 0.000) for 7161 atoms. Found 4 (34 requested) and removed 27 (17 requested) atoms. Cycle 20: After refmac, R = 0.1427 (Rfree = 0.000) for 7126 atoms. Found 1 (33 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 7354 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 7376 seeds are put forward Round 1: 397 peptides, 77 chains. Longest chain 14 peptides. Score 0.313 Round 2: 481 peptides, 80 chains. Longest chain 17 peptides. Score 0.416 Round 3: 461 peptides, 73 chains. Longest chain 20 peptides. Score 0.430 Round 4: 461 peptides, 72 chains. Longest chain 20 peptides. Score 0.436 Round 5: 468 peptides, 76 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 4 Chains 73, Residues 389, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17234 restraints for refining 7478 atoms. 15672 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1974 (Rfree = 0.000) for 7478 atoms. Found 25 (35 requested) and removed 56 (17 requested) atoms. Cycle 22: After refmac, R = 0.1856 (Rfree = 0.000) for 7401 atoms. Found 22 (35 requested) and removed 41 (17 requested) atoms. Cycle 23: After refmac, R = 0.1832 (Rfree = 0.000) for 7348 atoms. Found 28 (35 requested) and removed 39 (17 requested) atoms. Cycle 24: After refmac, R = 0.1716 (Rfree = 0.000) for 7306 atoms. Found 22 (34 requested) and removed 32 (17 requested) atoms. Cycle 25: After refmac, R = 0.1705 (Rfree = 0.000) for 7270 atoms. Found 17 (34 requested) and removed 36 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 7494 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7514 seeds are put forward Round 1: 374 peptides, 80 chains. Longest chain 10 peptides. Score 0.257 Round 2: 415 peptides, 73 chains. Longest chain 15 peptides. Score 0.366 Round 3: 408 peptides, 72 chains. Longest chain 15 peptides. Score 0.362 Round 4: 416 peptides, 71 chains. Longest chain 15 peptides. Score 0.380 Round 5: 426 peptides, 71 chains. Longest chain 15 peptides. Score 0.394 Taking the results from Round 5 Chains 71, Residues 355, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17701 restraints for refining 7488 atoms. 16352 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1925 (Rfree = 0.000) for 7488 atoms. Found 23 (35 requested) and removed 58 (17 requested) atoms. Cycle 27: After refmac, R = 0.1952 (Rfree = 0.000) for 7389 atoms. Found 30 (35 requested) and removed 38 (17 requested) atoms. Cycle 28: After refmac, R = 0.1960 (Rfree = 0.000) for 7349 atoms. Found 32 (35 requested) and removed 44 (17 requested) atoms. Cycle 29: After refmac, R = 0.1872 (Rfree = 0.000) for 7313 atoms. Found 28 (34 requested) and removed 39 (17 requested) atoms. Cycle 30: After refmac, R = 0.1832 (Rfree = 0.000) for 7273 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 7515 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 7539 seeds are put forward Round 1: 330 peptides, 74 chains. Longest chain 9 peptides. Score 0.226 Round 2: 400 peptides, 75 chains. Longest chain 12 peptides. Score 0.331 Round 3: 426 peptides, 74 chains. Longest chain 13 peptides. Score 0.375 Round 4: 415 peptides, 73 chains. Longest chain 16 peptides. Score 0.366 Round 5: 418 peptides, 74 chains. Longest chain 18 peptides. Score 0.364 Taking the results from Round 3 Chains 74, Residues 352, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17074 restraints for refining 7374 atoms. 15716 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1976 (Rfree = 0.000) for 7374 atoms. Found 26 (35 requested) and removed 45 (17 requested) atoms. Cycle 32: After refmac, R = 0.1941 (Rfree = 0.000) for 7316 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 33: After refmac, R = 0.1882 (Rfree = 0.000) for 7278 atoms. Found 28 (34 requested) and removed 35 (17 requested) atoms. Cycle 34: After refmac, R = 0.1907 (Rfree = 0.000) for 7243 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 35: After refmac, R = 0.1863 (Rfree = 0.000) for 7222 atoms. Found 22 (34 requested) and removed 35 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 7442 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 7454 seeds are put forward Round 1: 280 peptides, 59 chains. Longest chain 10 peptides. Score 0.247 Round 2: 366 peptides, 68 chains. Longest chain 14 peptides. Score 0.325 Round 3: 386 peptides, 69 chains. Longest chain 11 peptides. Score 0.349 Round 4: 396 peptides, 65 chains. Longest chain 15 peptides. Score 0.389 Round 5: 395 peptides, 62 chains. Longest chain 22 peptides. Score 0.406 Taking the results from Round 5 Chains 63, Residues 333, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17158 restraints for refining 7406 atoms. 15816 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1904 (Rfree = 0.000) for 7406 atoms. Found 17 (35 requested) and removed 71 (17 requested) atoms. Cycle 37: After refmac, R = 0.1792 (Rfree = 0.000) for 7321 atoms. Found 16 (34 requested) and removed 43 (17 requested) atoms. Cycle 38: After refmac, R = 0.1703 (Rfree = 0.000) for 7277 atoms. Found 13 (34 requested) and removed 37 (17 requested) atoms. Cycle 39: After refmac, R = 0.1638 (Rfree = 0.000) for 7235 atoms. Found 19 (34 requested) and removed 28 (17 requested) atoms. Cycle 40: After refmac, R = 0.1662 (Rfree = 0.000) for 7217 atoms. Found 13 (34 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 7418 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7435 seeds are put forward Round 1: 320 peptides, 69 chains. Longest chain 10 peptides. Score 0.244 Round 2: 359 peptides, 64 chains. Longest chain 10 peptides. Score 0.341 Round 3: 364 peptides, 61 chains. Longest chain 13 peptides. Score 0.368 Round 4: 373 peptides, 57 chains. Longest chain 16 peptides. Score 0.407 Round 5: 376 peptides, 60 chains. Longest chain 18 peptides. Score 0.392 Taking the results from Round 4 Chains 58, Residues 316, Estimated correctness of the model 0.0 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17179 restraints for refining 7429 atoms. 15865 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2042 (Rfree = 0.000) for 7429 atoms. Found 35 (35 requested) and removed 55 (17 requested) atoms. Cycle 42: After refmac, R = 0.1888 (Rfree = 0.000) for 7373 atoms. Found 23 (35 requested) and removed 41 (17 requested) atoms. Cycle 43: After refmac, R = 0.2035 (Rfree = 0.000) for 7322 atoms. Found 34 (34 requested) and removed 45 (17 requested) atoms. Cycle 44: After refmac, R = 0.1457 (Rfree = 0.000) for 7294 atoms. Found 7 (34 requested) and removed 24 (17 requested) atoms. Cycle 45: After refmac, R = 0.1366 (Rfree = 0.000) for 7269 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 7483 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7496 seeds are put forward Round 1: 299 peptides, 67 chains. Longest chain 8 peptides. Score 0.222 Round 2: 351 peptides, 68 chains. Longest chain 12 peptides. Score 0.301 Round 3: 357 peptides, 67 chains. Longest chain 14 peptides. Score 0.317 Round 4: 350 peptides, 65 chains. Longest chain 13 peptides. Score 0.320 Round 5: 366 peptides, 65 chains. Longest chain 16 peptides. Score 0.344 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 301, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vl5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9787 reflections ( 99.93 % complete ) and 17715 restraints for refining 7424 atoms. 16576 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2019 (Rfree = 0.000) for 7424 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2004 (Rfree = 0.000) for 7366 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1881 (Rfree = 0.000) for 7326 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1992 (Rfree = 0.000) for 7298 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:08:57 GMT 2018 Job finished. TimeTaking 101.01 Used memory is bytes: 16719600