null Tue 25 Dec 19:27:55 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 1vl4-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-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/1vl4-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-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 ============================================================ Tue 25 Dec 19:28:05 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/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-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 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-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-3.6-parrot-hancs.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 7952 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3050 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3035 (Rfree = 0.000) for 7952 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.21 Search for helices and strands: 0 residues in 0 chains, 8051 seeds are put forward NCS extension: 0 residues added, 8051 seeds are put forward Round 1: 376 peptides, 67 chains. Longest chain 19 peptides. Score 0.362 Round 2: 504 peptides, 76 chains. Longest chain 19 peptides. Score 0.496 Round 3: 522 peptides, 70 chains. Longest chain 22 peptides. Score 0.555 Round 4: 562 peptides, 66 chains. Longest chain 23 peptides. Score 0.624 Round 5: 566 peptides, 67 chains. Longest chain 29 peptides. Score 0.623 Taking the results from Round 4 Chains 69, Residues 496, Estimated correctness of the model 23.8 % 9 chains (87 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 13456 restraints for refining 6481 atoms. 11255 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2670 (Rfree = 0.000) for 6481 atoms. Found 23 (41 requested) and removed 56 (20 requested) atoms. Cycle 2: After refmac, R = 0.2452 (Rfree = 0.000) for 6338 atoms. Found 27 (41 requested) and removed 47 (20 requested) atoms. Cycle 3: After refmac, R = 0.2368 (Rfree = 0.000) for 6271 atoms. Found 25 (40 requested) and removed 37 (20 requested) atoms. Cycle 4: After refmac, R = 0.2263 (Rfree = 0.000) for 6234 atoms. Found 17 (40 requested) and removed 37 (20 requested) atoms. Cycle 5: After refmac, R = 0.2212 (Rfree = 0.000) for 6197 atoms. Found 11 (39 requested) and removed 33 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.20 Search for helices and strands: 0 residues in 0 chains, 6392 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6415 seeds are put forward Round 1: 495 peptides, 78 chains. Longest chain 21 peptides. Score 0.471 Round 2: 576 peptides, 73 chains. Longest chain 26 peptides. Score 0.604 Round 3: 555 peptides, 66 chains. Longest chain 24 peptides. Score 0.616 Round 4: 562 peptides, 68 chains. Longest chain 24 peptides. Score 0.614 Round 5: 573 peptides, 64 chains. Longest chain 27 peptides. Score 0.646 Taking the results from Round 5 Chains 71, Residues 509, Estimated correctness of the model 31.8 % 7 chains (107 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 13042 restraints for refining 6482 atoms. 10640 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2684 (Rfree = 0.000) for 6482 atoms. Found 41 (41 requested) and removed 50 (20 requested) atoms. Cycle 7: After refmac, R = 0.2421 (Rfree = 0.000) for 6371 atoms. Found 34 (41 requested) and removed 42 (20 requested) atoms. Cycle 8: After refmac, R = 0.2252 (Rfree = 0.000) for 6326 atoms. Found 16 (40 requested) and removed 37 (20 requested) atoms. Cycle 9: After refmac, R = 0.2148 (Rfree = 0.000) for 6283 atoms. Found 14 (40 requested) and removed 30 (20 requested) atoms. Cycle 10: After refmac, R = 0.2083 (Rfree = 0.000) for 6256 atoms. Found 8 (40 requested) and removed 31 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 6406 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6432 seeds are put forward Round 1: 481 peptides, 72 chains. Longest chain 20 peptides. Score 0.489 Round 2: 538 peptides, 64 chains. Longest chain 25 peptides. Score 0.607 Round 3: 553 peptides, 62 chains. Longest chain 32 peptides. Score 0.634 Round 4: 560 peptides, 66 chains. Longest chain 26 peptides. Score 0.622 Round 5: 560 peptides, 63 chains. Longest chain 27 peptides. Score 0.637 Taking the results from Round 5 Chains 70, Residues 497, Estimated correctness of the model 28.5 % 11 chains (105 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 13461 restraints for refining 6483 atoms. 11160 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2414 (Rfree = 0.000) for 6483 atoms. Found 28 (41 requested) and removed 55 (20 requested) atoms. Cycle 12: After refmac, R = 0.2268 (Rfree = 0.000) for 6396 atoms. Found 22 (41 requested) and removed 35 (20 requested) atoms. Cycle 13: After refmac, R = 0.2280 (Rfree = 0.000) for 6355 atoms. Found 24 (40 requested) and removed 38 (20 requested) atoms. Cycle 14: After refmac, R = 0.2288 (Rfree = 0.000) for 6327 atoms. Found 28 (40 requested) and removed 32 (20 requested) atoms. Cycle 15: After refmac, R = 0.2210 (Rfree = 0.000) for 6313 atoms. Found 17 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 6466 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6486 seeds are put forward Round 1: 476 peptides, 73 chains. Longest chain 19 peptides. Score 0.475 Round 2: 502 peptides, 68 chains. Longest chain 22 peptides. Score 0.541 Round 3: 503 peptides, 67 chains. Longest chain 24 peptides. Score 0.548 Round 4: 509 peptides, 70 chains. Longest chain 31 peptides. Score 0.538 Round 5: 524 peptides, 69 chains. Longest chain 26 peptides. Score 0.563 Taking the results from Round 5 Chains 72, Residues 455, Estimated correctness of the model 0.0 % 8 chains (73 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14106 restraints for refining 6483 atoms. 12122 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2438 (Rfree = 0.000) for 6483 atoms. Found 38 (41 requested) and removed 53 (20 requested) atoms. Cycle 17: After refmac, R = 0.2262 (Rfree = 0.000) for 6412 atoms. Found 33 (41 requested) and removed 33 (20 requested) atoms. Cycle 18: After refmac, R = 0.2177 (Rfree = 0.000) for 6385 atoms. Found 27 (41 requested) and removed 34 (20 requested) atoms. Cycle 19: After refmac, R = 0.2107 (Rfree = 0.000) for 6355 atoms. Found 18 (40 requested) and removed 26 (20 requested) atoms. Cycle 20: After refmac, R = 0.2106 (Rfree = 0.000) for 6328 atoms. Found 23 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.19 Search for helices and strands: 0 residues in 0 chains, 6492 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 6528 seeds are put forward Round 1: 432 peptides, 72 chains. Longest chain 17 peptides. Score 0.417 Round 2: 457 peptides, 63 chains. Longest chain 25 peptides. Score 0.511 Round 3: 470 peptides, 62 chains. Longest chain 23 peptides. Score 0.534 Round 4: 460 peptides, 58 chains. Longest chain 32 peptides. Score 0.545 Round 5: 472 peptides, 62 chains. Longest chain 49 peptides. Score 0.537 Taking the results from Round 4 Chains 62, Residues 402, Estimated correctness of the model 0.0 % 4 chains (64 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14133 restraints for refining 6483 atoms. 12341 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2255 (Rfree = 0.000) for 6483 atoms. Found 21 (41 requested) and removed 33 (20 requested) atoms. Cycle 22: After refmac, R = 0.2070 (Rfree = 0.000) for 6412 atoms. Found 10 (41 requested) and removed 28 (20 requested) atoms. Cycle 23: After refmac, R = 0.1995 (Rfree = 0.000) for 6375 atoms. Found 3 (41 requested) and removed 27 (20 requested) atoms. Cycle 24: After refmac, R = 0.1952 (Rfree = 0.000) for 6344 atoms. Found 5 (40 requested) and removed 22 (20 requested) atoms. Cycle 25: After refmac, R = 0.1950 (Rfree = 0.000) for 6321 atoms. Found 5 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6457 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6481 seeds are put forward Round 1: 405 peptides, 74 chains. Longest chain 18 peptides. Score 0.361 Round 2: 442 peptides, 60 chains. Longest chain 22 peptides. Score 0.509 Round 3: 440 peptides, 61 chains. Longest chain 17 peptides. Score 0.500 Round 4: 436 peptides, 63 chains. Longest chain 20 peptides. Score 0.481 Round 5: 443 peptides, 60 chains. Longest chain 25 peptides. Score 0.510 Taking the results from Round 5 Chains 63, Residues 383, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14563 restraints for refining 6483 atoms. 12933 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2369 (Rfree = 0.000) for 6483 atoms. Found 15 (41 requested) and removed 57 (20 requested) atoms. Cycle 27: After refmac, R = 0.2246 (Rfree = 0.000) for 6422 atoms. Found 27 (41 requested) and removed 32 (20 requested) atoms. Cycle 28: After refmac, R = 0.2297 (Rfree = 0.000) for 6403 atoms. Found 31 (41 requested) and removed 34 (20 requested) atoms. Cycle 29: After refmac, R = 0.2175 (Rfree = 0.000) for 6393 atoms. Found 23 (41 requested) and removed 26 (20 requested) atoms. Cycle 30: After refmac, R = 0.2051 (Rfree = 0.000) for 6376 atoms. Found 8 (40 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 6504 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6527 seeds are put forward Round 1: 385 peptides, 68 chains. Longest chain 18 peptides. Score 0.370 Round 2: 421 peptides, 65 chains. Longest chain 22 peptides. Score 0.447 Round 3: 448 peptides, 68 chains. Longest chain 17 peptides. Score 0.467 Round 4: 435 peptides, 60 chains. Longest chain 23 peptides. Score 0.499 Round 5: 431 peptides, 63 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 4 Chains 62, Residues 375, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14755 restraints for refining 6483 atoms. 13253 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2366 (Rfree = 0.000) for 6483 atoms. Found 38 (41 requested) and removed 42 (20 requested) atoms. Cycle 32: After refmac, R = 0.2317 (Rfree = 0.000) for 6461 atoms. Found 41 (41 requested) and removed 28 (20 requested) atoms. Cycle 33: After refmac, R = 0.2378 (Rfree = 0.000) for 6462 atoms. Found 41 (41 requested) and removed 42 (20 requested) atoms. Cycle 34: After refmac, R = 0.2029 (Rfree = 0.000) for 6452 atoms. Found 7 (41 requested) and removed 24 (20 requested) atoms. Cycle 35: After refmac, R = 0.2061 (Rfree = 0.000) for 6429 atoms. Found 8 (41 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 6543 seeds are put forward NCS extension: 48 residues added (1 deleted due to clashes), 6591 seeds are put forward Round 1: 377 peptides, 74 chains. Longest chain 12 peptides. Score 0.314 Round 2: 411 peptides, 67 chains. Longest chain 15 peptides. Score 0.418 Round 3: 410 peptides, 68 chains. Longest chain 14 peptides. Score 0.410 Round 4: 444 peptides, 63 chains. Longest chain 16 peptides. Score 0.493 Round 5: 423 peptides, 60 chains. Longest chain 17 peptides. Score 0.482 Taking the results from Round 4 Chains 64, Residues 381, Estimated correctness of the model 0.0 % 7 chains (46 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14649 restraints for refining 6481 atoms. 13031 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2429 (Rfree = 0.000) for 6481 atoms. Found 29 (41 requested) and removed 31 (20 requested) atoms. Cycle 37: After refmac, R = 0.2340 (Rfree = 0.000) for 6448 atoms. Found 41 (41 requested) and removed 28 (20 requested) atoms. Cycle 38: After refmac, R = 0.2151 (Rfree = 0.000) for 6443 atoms. Found 30 (41 requested) and removed 30 (20 requested) atoms. Cycle 39: After refmac, R = 0.2177 (Rfree = 0.000) for 6425 atoms. Found 30 (41 requested) and removed 24 (20 requested) atoms. Cycle 40: After refmac, R = 0.2125 (Rfree = 0.000) for 6415 atoms. Found 37 (41 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.22 Search for helices and strands: 0 residues in 0 chains, 6563 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6582 seeds are put forward Round 1: 356 peptides, 70 chains. Longest chain 13 peptides. Score 0.307 Round 2: 396 peptides, 63 chains. Longest chain 16 peptides. Score 0.422 Round 3: 383 peptides, 58 chains. Longest chain 15 peptides. Score 0.436 Round 4: 380 peptides, 63 chains. Longest chain 16 peptides. Score 0.397 Round 5: 391 peptides, 58 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 5 Chains 58, Residues 333, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 15171 restraints for refining 6483 atoms. 13808 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2246 (Rfree = 0.000) for 6483 atoms. Found 31 (41 requested) and removed 34 (20 requested) atoms. Cycle 42: After refmac, R = 0.2091 (Rfree = 0.000) for 6462 atoms. Found 11 (41 requested) and removed 34 (20 requested) atoms. Cycle 43: After refmac, R = 0.2054 (Rfree = 0.000) for 6433 atoms. Found 18 (41 requested) and removed 27 (20 requested) atoms. Cycle 44: After refmac, R = 0.2001 (Rfree = 0.000) for 6418 atoms. Found 21 (41 requested) and removed 27 (20 requested) atoms. Cycle 45: After refmac, R = 0.1983 (Rfree = 0.000) for 6411 atoms. Found 19 (41 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 6546 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6559 seeds are put forward Round 1: 348 peptides, 65 chains. Longest chain 14 peptides. Score 0.330 Round 2: 397 peptides, 65 chains. Longest chain 16 peptides. Score 0.410 Round 3: 384 peptides, 60 chains. Longest chain 14 peptides. Score 0.424 Round 4: 399 peptides, 61 chains. Longest chain 17 peptides. Score 0.440 Round 5: 386 peptides, 56 chains. Longest chain 20 peptides. Score 0.454 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 330, Estimated correctness of the model 0.0 % 7 chains (37 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (330 residues) following loop building 7 chains (37 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12391 reflections ( 99.37 % complete ) and 15024 restraints for refining 6481 atoms. 13643 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2147 (Rfree = 0.000) for 6481 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2090 (Rfree = 0.000) for 6443 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2007 (Rfree = 0.000) for 6413 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.2047 (Rfree = 0.000) for 6387 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:01:46 GMT 2018 Job finished. TimeTaking 93.84 Used memory is bytes: 20106392