null Sun 23 Dec 22:22:43 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 1vr0-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.6-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/1vr0-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.6-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 ============================================================ Sun 23 Dec 22:22:53 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/1vr0-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.6-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 495 and 0 Target number of residues in the AU: 495 Target solvent content: 0.6343 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-3.6-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 5928 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: 226.759 3.600 Wilson plot Bfac: 68.71 9023 reflections ( 99.64 % complete ) and 0 restraints for refining 6590 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3220 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3173 (Rfree = 0.000) for 6590 atoms. Found 42 (42 requested) and removed 47 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 6707 seeds are put forward NCS extension: 0 residues added, 6707 seeds are put forward Round 1: 285 peptides, 59 chains. Longest chain 9 peptides. Score 0.291 Round 2: 350 peptides, 57 chains. Longest chain 12 peptides. Score 0.454 Round 3: 390 peptides, 57 chains. Longest chain 19 peptides. Score 0.531 Round 4: 381 peptides, 55 chains. Longest chain 14 peptides. Score 0.531 Round 5: 391 peptides, 49 chains. Longest chain 19 peptides. Score 0.595 Taking the results from Round 5 Chains 49, Residues 342, Estimated correctness of the model 12.7 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12366 restraints for refining 5372 atoms. 10984 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2525 (Rfree = 0.000) for 5372 atoms. Found 31 (34 requested) and removed 49 (17 requested) atoms. Cycle 2: After refmac, R = 0.2377 (Rfree = 0.000) for 5268 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 3: After refmac, R = 0.2288 (Rfree = 0.000) for 5219 atoms. Found 32 (33 requested) and removed 30 (16 requested) atoms. Cycle 4: After refmac, R = 0.2169 (Rfree = 0.000) for 5188 atoms. Found 27 (33 requested) and removed 28 (16 requested) atoms. Cycle 5: After refmac, R = 0.2143 (Rfree = 0.000) for 5164 atoms. Found 28 (33 requested) and removed 34 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.57 Search for helices and strands: 0 residues in 0 chains, 5381 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 5400 seeds are put forward Round 1: 329 peptides, 61 chains. Longest chain 16 peptides. Score 0.373 Round 2: 368 peptides, 58 chains. Longest chain 19 peptides. Score 0.481 Round 3: 400 peptides, 60 chains. Longest chain 20 peptides. Score 0.525 Round 4: 386 peptides, 54 chains. Longest chain 19 peptides. Score 0.548 Round 5: 402 peptides, 54 chains. Longest chain 20 peptides. Score 0.576 Taking the results from Round 5 Chains 54, Residues 348, Estimated correctness of the model 5.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12198 restraints for refining 5281 atoms. 10860 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2191 (Rfree = 0.000) for 5281 atoms. Found 21 (33 requested) and removed 49 (16 requested) atoms. Cycle 7: After refmac, R = 0.2053 (Rfree = 0.000) for 5227 atoms. Found 29 (33 requested) and removed 27 (16 requested) atoms. Cycle 8: After refmac, R = 0.2009 (Rfree = 0.000) for 5212 atoms. Found 21 (33 requested) and removed 33 (16 requested) atoms. Cycle 9: After refmac, R = 0.1651 (Rfree = 0.000) for 5193 atoms. Found 9 (33 requested) and removed 30 (16 requested) atoms. Cycle 10: After refmac, R = 0.1599 (Rfree = 0.000) for 5169 atoms. Found 1 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 5331 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5357 seeds are put forward Round 1: 361 peptides, 65 chains. Longest chain 16 peptides. Score 0.405 Round 2: 382 peptides, 56 chains. Longest chain 19 peptides. Score 0.525 Round 3: 362 peptides, 49 chains. Longest chain 24 peptides. Score 0.545 Round 4: 397 peptides, 54 chains. Longest chain 19 peptides. Score 0.567 Round 5: 411 peptides, 54 chains. Longest chain 22 peptides. Score 0.591 Taking the results from Round 5 Chains 55, Residues 357, Estimated correctness of the model 11.1 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12273 restraints for refining 5373 atoms. 10853 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2228 (Rfree = 0.000) for 5373 atoms. Found 29 (34 requested) and removed 51 (17 requested) atoms. Cycle 12: After refmac, R = 0.2155 (Rfree = 0.000) for 5329 atoms. Found 25 (34 requested) and removed 36 (17 requested) atoms. Cycle 13: After refmac, R = 0.2102 (Rfree = 0.000) for 5304 atoms. Found 34 (34 requested) and removed 41 (17 requested) atoms. Cycle 14: After refmac, R = 0.1739 (Rfree = 0.000) for 5288 atoms. Found 14 (33 requested) and removed 24 (16 requested) atoms. Cycle 15: After refmac, R = 0.1704 (Rfree = 0.000) for 5273 atoms. Found 11 (33 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 5461 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5474 seeds are put forward Round 1: 381 peptides, 63 chains. Longest chain 17 peptides. Score 0.464 Round 2: 401 peptides, 54 chains. Longest chain 24 peptides. Score 0.574 Round 3: 409 peptides, 56 chains. Longest chain 27 peptides. Score 0.572 Round 4: 407 peptides, 49 chains. Longest chain 35 peptides. Score 0.620 Round 5: 399 peptides, 51 chains. Longest chain 25 peptides. Score 0.593 Taking the results from Round 4 Chains 49, Residues 358, Estimated correctness of the model 22.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12367 restraints for refining 5373 atoms. 10984 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2232 (Rfree = 0.000) for 5373 atoms. Found 28 (34 requested) and removed 32 (17 requested) atoms. Cycle 17: After refmac, R = 0.2192 (Rfree = 0.000) for 5350 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 18: After refmac, R = 0.2161 (Rfree = 0.000) for 5338 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 19: After refmac, R = 0.2161 (Rfree = 0.000) for 5335 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 20: After refmac, R = 0.1758 (Rfree = 0.000) for 5326 atoms. Found 7 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.66 Search for helices and strands: 0 residues in 0 chains, 5503 seeds are put forward NCS extension: 20 residues added (10 deleted due to clashes), 5523 seeds are put forward Round 1: 325 peptides, 57 chains. Longest chain 16 peptides. Score 0.401 Round 2: 368 peptides, 54 chains. Longest chain 20 peptides. Score 0.515 Round 3: 357 peptides, 53 chains. Longest chain 18 peptides. Score 0.502 Round 4: 357 peptides, 52 chains. Longest chain 18 peptides. Score 0.511 Round 5: 367 peptides, 54 chains. Longest chain 29 peptides. Score 0.513 Taking the results from Round 2 Chains 54, Residues 314, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12517 restraints for refining 5373 atoms. 11315 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2020 (Rfree = 0.000) for 5373 atoms. Found 18 (34 requested) and removed 41 (17 requested) atoms. Cycle 22: After refmac, R = 0.1925 (Rfree = 0.000) for 5338 atoms. Found 22 (34 requested) and removed 22 (17 requested) atoms. Cycle 23: After refmac, R = 0.1658 (Rfree = 0.000) for 5329 atoms. Found 3 (34 requested) and removed 22 (17 requested) atoms. Cycle 24: After refmac, R = 0.1569 (Rfree = 0.000) for 5305 atoms. Found 2 (34 requested) and removed 24 (17 requested) atoms. Cycle 25: After refmac, R = 0.1547 (Rfree = 0.000) for 5281 atoms. Found 3 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 5441 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 5453 seeds are put forward Round 1: 301 peptides, 58 chains. Longest chain 12 peptides. Score 0.338 Round 2: 351 peptides, 55 chains. Longest chain 16 peptides. Score 0.473 Round 3: 353 peptides, 53 chains. Longest chain 28 peptides. Score 0.494 Round 4: 362 peptides, 53 chains. Longest chain 16 peptides. Score 0.512 Round 5: 332 peptides, 49 chains. Longest chain 18 peptides. Score 0.488 Taking the results from Round 4 Chains 55, Residues 309, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12450 restraints for refining 5373 atoms. 11230 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2060 (Rfree = 0.000) for 5373 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 27: After refmac, R = 0.2105 (Rfree = 0.000) for 5358 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 28: After refmac, R = 0.1696 (Rfree = 0.000) for 5350 atoms. Found 3 (34 requested) and removed 21 (17 requested) atoms. Cycle 29: After refmac, R = 0.1627 (Rfree = 0.000) for 5326 atoms. Found 4 (34 requested) and removed 25 (17 requested) atoms. Cycle 30: After refmac, R = 0.1602 (Rfree = 0.000) for 5303 atoms. Found 3 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 5453 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5468 seeds are put forward Round 1: 294 peptides, 55 chains. Longest chain 12 peptides. Score 0.351 Round 2: 303 peptides, 49 chains. Longest chain 19 peptides. Score 0.428 Round 3: 313 peptides, 50 chains. Longest chain 15 peptides. Score 0.440 Round 4: 320 peptides, 47 chains. Longest chain 18 peptides. Score 0.482 Round 5: 308 peptides, 45 chains. Longest chain 19 peptides. Score 0.475 Taking the results from Round 4 Chains 47, Residues 273, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12779 restraints for refining 5373 atoms. 11734 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2092 (Rfree = 0.000) for 5373 atoms. Found 23 (34 requested) and removed 24 (17 requested) atoms. Cycle 32: After refmac, R = 0.2094 (Rfree = 0.000) for 5353 atoms. Found 27 (34 requested) and removed 27 (17 requested) atoms. Cycle 33: After refmac, R = 0.1659 (Rfree = 0.000) for 5343 atoms. Found 8 (34 requested) and removed 22 (17 requested) atoms. Cycle 34: After refmac, R = 0.1591 (Rfree = 0.000) for 5324 atoms. Found 3 (34 requested) and removed 22 (17 requested) atoms. Cycle 35: After refmac, R = 0.1582 (Rfree = 0.000) for 5304 atoms. Found 0 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 5462 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5480 seeds are put forward Round 1: 254 peptides, 55 chains. Longest chain 9 peptides. Score 0.255 Round 2: 295 peptides, 49 chains. Longest chain 19 peptides. Score 0.411 Round 3: 312 peptides, 50 chains. Longest chain 19 peptides. Score 0.438 Round 4: 311 peptides, 54 chains. Longest chain 12 peptides. Score 0.399 Round 5: 311 peptides, 50 chains. Longest chain 19 peptides. Score 0.436 Taking the results from Round 3 Chains 50, Residues 262, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12808 restraints for refining 5372 atoms. 11810 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2073 (Rfree = 0.000) for 5372 atoms. Found 30 (34 requested) and removed 30 (17 requested) atoms. Cycle 37: After refmac, R = 0.2080 (Rfree = 0.000) for 5358 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 38: After refmac, R = 0.2013 (Rfree = 0.000) for 5356 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 39: After refmac, R = 0.1974 (Rfree = 0.000) for 5354 atoms. Found 28 (34 requested) and removed 19 (17 requested) atoms. Cycle 40: After refmac, R = 0.1603 (Rfree = 0.000) for 5357 atoms. Found 10 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 5530 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 5559 seeds are put forward Round 1: 243 peptides, 51 chains. Longest chain 9 peptides. Score 0.269 Round 2: 291 peptides, 46 chains. Longest chain 18 peptides. Score 0.431 Round 3: 282 peptides, 49 chains. Longest chain 13 peptides. Score 0.382 Round 4: 285 peptides, 45 chains. Longest chain 19 peptides. Score 0.427 Round 5: 291 peptides, 47 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 2 Chains 46, Residues 245, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12699 restraints for refining 5373 atoms. 11765 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1978 (Rfree = 0.000) for 5373 atoms. Found 22 (34 requested) and removed 25 (17 requested) atoms. Cycle 42: After refmac, R = 0.2064 (Rfree = 0.000) for 5358 atoms. Found 33 (34 requested) and removed 24 (17 requested) atoms. Cycle 43: After refmac, R = 0.2061 (Rfree = 0.000) for 5355 atoms. Found 34 (34 requested) and removed 21 (17 requested) atoms. Cycle 44: After refmac, R = 0.1629 (Rfree = 0.000) for 5362 atoms. Found 3 (34 requested) and removed 19 (17 requested) atoms. Cycle 45: After refmac, R = 0.2053 (Rfree = 0.000) for 5343 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 5506 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 5527 seeds are put forward Round 1: 212 peptides, 42 chains. Longest chain 10 peptides. Score 0.287 Round 2: 234 peptides, 40 chains. Longest chain 12 peptides. Score 0.362 Round 3: 249 peptides, 42 chains. Longest chain 12 peptides. Score 0.377 Round 4: 248 peptides, 41 chains. Longest chain 18 peptides. Score 0.384 Round 5: 246 peptides, 42 chains. Longest chain 12 peptides. Score 0.370 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 207, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vr0-3_warpNtrace.pdb as input Building loops using Loopy2018 41 chains (207 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9023 reflections ( 99.64 % complete ) and 12603 restraints for refining 5330 atoms. 11802 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2236 (Rfree = 0.000) for 5330 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2153 (Rfree = 0.000) for 5305 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2075 (Rfree = 0.000) for 5272 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2140 (Rfree = 0.000) for 5250 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:40:33 GMT 2018 Job finished. TimeTaking 77.84 Used memory is bytes: 15229208