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 1vk3-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.2-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/1vk3-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.2-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 19:28:07 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/1vk3-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.2-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 471 and 0 Target number of residues in the AU: 471 Target solvent content: 0.5437 Checking the provided sequence file Detected sequence length: 615 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 615 Adjusted target solvent content: 0.40 Input MTZ file: 1vk3-3.2-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: 59.785 72.683 128.550 90.000 90.000 90.000 Input sequence file: 1vk3-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4920 target number of atoms Had to go as low as 0.55 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 Loops will be built when appropriate and at the last cycle Resolution range: 30.186 3.200 Wilson plot Bfac: 33.83 9600 reflections ( 98.60 % complete ) and 0 restraints for refining 5421 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3201 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2552 (Rfree = 0.000) for 5421 atoms. Found 45 (48 requested) and removed 57 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.71 3.10 Search for helices and strands: 0 residues in 0 chains, 5503 seeds are put forward Round 1: 219 peptides, 45 chains. Longest chain 10 peptides. Score 0.296 Round 2: 283 peptides, 50 chains. Longest chain 13 peptides. Score 0.421 Round 3: 294 peptides, 50 chains. Longest chain 15 peptides. Score 0.451 Round 4: 323 peptides, 52 chains. Longest chain 17 peptides. Score 0.503 Round 5: 299 peptides, 47 chains. Longest chain 14 peptides. Score 0.497 Taking the results from Round 4 Chains 53, Residues 271, Estimated correctness of the model 12.3 % 12 chains (70 residues) have been docked in sequence ------------------------------------------------------ 9600 reflections ( 98.60 % complete ) and 9652 restraints for refining 4491 atoms. 8453 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2559 (Rfree = 0.000) for 4491 atoms. Found 32 (40 requested) and removed 51 (20 requested) atoms. Cycle 2: After refmac, R = 0.2378 (Rfree = 0.000) for 4414 atoms. Found 24 (40 requested) and removed 32 (20 requested) atoms. Cycle 3: After refmac, R = 0.2286 (Rfree = 0.000) for 4379 atoms. Found 18 (39 requested) and removed 26 (19 requested) atoms. Cycle 4: After refmac, R = 0.2264 (Rfree = 0.000) for 4348 atoms. Found 23 (39 requested) and removed 27 (19 requested) atoms. Cycle 5: After refmac, R = 0.2173 (Rfree = 0.000) for 4326 atoms. Found 22 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.72 3.11 Search for helices and strands: 0 residues in 0 chains, 4453 seeds are put forward Round 1: 316 peptides, 58 chains. Longest chain 19 peptides. Score 0.419 Round 2: 322 peptides, 52 chains. Longest chain 20 peptides. Score 0.501 Round 3: 339 peptides, 52 chains. Longest chain 17 peptides. Score 0.541 Round 4: 345 peptides, 49 chains. Longest chain 20 peptides. Score 0.584 Round 5: 349 peptides, 49 chains. Longest chain 20 peptides. Score 0.592 Taking the results from Round 5 Chains 49, Residues 300, Estimated correctness of the model 38.9 % 5 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9600 reflections ( 98.60 % complete ) and 9678 restraints for refining 4372 atoms. 8493 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2381 (Rfree = 0.000) for 4372 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. Cycle 7: After refmac, R = 0.2134 (Rfree = 0.000) for 4355 atoms. Found 22 (39 requested) and removed 28 (19 requested) atoms. Cycle 8: After refmac, R = 0.2018 (Rfree = 0.000) for 4338 atoms. Found 22 (39 requested) and removed 23 (19 requested) atoms. Cycle 9: After refmac, R = 0.1958 (Rfree = 0.000) for 4325 atoms. Found 15 (38 requested) and removed 19 (19 requested) atoms. Cycle 10: After refmac, R = 0.1933 (Rfree = 0.000) for 4312 atoms. Found 19 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.73 3.12 Search for helices and strands: 0 residues in 0 chains, 4452 seeds are put forward Round 1: 309 peptides, 57 chains. Longest chain 12 peptides. Score 0.412 Round 2: 321 peptides, 49 chains. Longest chain 14 peptides. Score 0.529 Round 3: 328 peptides, 48 chains. Longest chain 16 peptides. Score 0.556 Round 4: 321 peptides, 43 chains. Longest chain 17 peptides. Score 0.589 Round 5: 334 peptides, 46 chains. Longest chain 19 peptides. Score 0.588 Taking the results from Round 4 Chains 44, Residues 278, Estimated correctness of the model 38.1 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 9600 reflections ( 98.60 % complete ) and 9514 restraints for refining 4370 atoms. 8339 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2218 (Rfree = 0.000) for 4370 atoms. Found 34 (39 requested) and removed 39 (19 requested) atoms. Cycle 12: After refmac, R = 0.2085 (Rfree = 0.000) for 4346 atoms. Found 19 (39 requested) and removed 23 (19 requested) atoms. Cycle 13: After refmac, R = 0.2018 (Rfree = 0.000) for 4329 atoms. Found 19 (38 requested) and removed 25 (19 requested) atoms. Cycle 14: After refmac, R = 0.1968 (Rfree = 0.000) for 4313 atoms. Found 19 (38 requested) and removed 22 (19 requested) atoms. Cycle 15: After refmac, R = 0.1899 (Rfree = 0.000) for 4303 atoms. Found 16 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.74 3.14 Search for helices and strands: 0 residues in 0 chains, 4424 seeds are put forward Round 1: 291 peptides, 51 chains. Longest chain 16 peptides. Score 0.432 Round 2: 334 peptides, 50 chains. Longest chain 17 peptides. Score 0.550 Round 3: 330 peptides, 50 chains. Longest chain 21 peptides. Score 0.540 Round 4: 341 peptides, 49 chains. Longest chain 20 peptides. Score 0.575 Round 5: 324 peptides, 46 chains. Longest chain 21 peptides. Score 0.567 Taking the results from Round 4 Chains 49, Residues 292, Estimated correctness of the model 34.1 % 6 chains (37 residues) have been docked in sequence ------------------------------------------------------ 9600 reflections ( 98.60 % complete ) and 9531 restraints for refining 4405 atoms. 8324 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2181 (Rfree = 0.000) for 4405 atoms. Found 35 (39 requested) and removed 41 (19 requested) atoms. Cycle 17: After refmac, R = 0.1996 (Rfree = 0.000) for 4382 atoms. Found 15 (39 requested) and removed 27 (19 requested) atoms. Cycle 18: After refmac, R = 0.1934 (Rfree = 0.000) for 4364 atoms. Found 16 (39 requested) and removed 23 (19 requested) atoms. Cycle 19: After refmac, R = 0.1903 (Rfree = 0.000) for 4354 atoms. Found 14 (39 requested) and removed 22 (19 requested) atoms. Cycle 20: After refmac, R = 0.1861 (Rfree = 0.000) for 4345 atoms. Found 9 (39 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.75 3.15 Search for helices and strands: 0 residues in 0 chains, 4457 seeds are put forward Round 1: 279 peptides, 51 chains. Longest chain 11 peptides. Score 0.399 Round 2: 317 peptides, 50 chains. Longest chain 16 peptides. Score 0.509 Round 3: 312 peptides, 46 chains. Longest chain 17 peptides. Score 0.539 Round 4: 295 peptides, 43 chains. Longest chain 16 peptides. Score 0.530 Round 5: 303 peptides, 44 chains. Longest chain 22 peptides. Score 0.539 Taking the results from Round 5 Chains 48, Residues 259, Estimated correctness of the model 23.6 % 9 chains (61 residues) have been docked in sequence ------------------------------------------------------ 9600 reflections ( 98.60 % complete ) and 9609 restraints for refining 4464 atoms. 8459 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2219 (Rfree = 0.000) for 4464 atoms. Found 40 (40 requested) and removed 35 (20 requested) atoms. Cycle 22: After refmac, R = 0.1962 (Rfree = 0.000) for 4465 atoms. Found 15 (40 requested) and removed 31 (20 requested) atoms. Cycle 23: After refmac, R = 0.1907 (Rfree = 0.000) for 4439 atoms. Found 11 (39 requested) and removed 23 (19 requested) atoms. Cycle 24: After refmac, R = 0.1889 (Rfree = 0.000) for 4425 atoms. Found 13 (39 requested) and removed 22 (19 requested) atoms. Cycle 25: After refmac, R = 0.1872 (Rfree = 0.000) for 4410 atoms. Found 11 (39 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.74 3.14 Search for helices and strands: 0 residues in 0 chains, 4504 seeds are put forward Round 1: 278 peptides, 48 chains. Longest chain 20 peptides. Score 0.431 Round 2: 311 peptides, 48 chains. Longest chain 17 peptides. Score 0.516 Round 3: 289 peptides, 40 chains. Longest chain 24 peptides. Score 0.547 Round 4: 304 peptides, 43 chains. Longest chain 22 peptides. Score 0.551 Round 5: 302 peptides, 43 chains. Longest chain 24 peptides. Score 0.546 Taking the results from Round 4 Chains 44, Residues 261, Estimated correctness of the model 27.2 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9600 reflections ( 98.60 % complete ) and 9863 restraints for refining 4491 atoms. 8729 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2073 (Rfree = 0.000) for 4491 atoms. Found 39 (40 requested) and removed 30 (20 requested) atoms. Cycle 27: After refmac, R = 0.1937 (Rfree = 0.000) for 4491 atoms. Found 23 (40 requested) and removed 28 (20 requested) atoms. Cycle 28: After refmac, R = 0.1857 (Rfree = 0.000) for 4478 atoms. Found 24 (40 requested) and removed 22 (20 requested) atoms. Cycle 29: After refmac, R = 0.1784 (Rfree = 0.000) for 4474 atoms. Found 17 (40 requested) and removed 22 (20 requested) atoms. Cycle 30: After refmac, R = 0.1742 (Rfree = 0.000) for 4467 atoms. Found 13 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.75 3.15 Search for helices and strands: 0 residues in 0 chains, 4542 seeds are put forward Round 1: 255 peptides, 44 chains. Longest chain 14 peptides. Score 0.415 Round 2: 300 peptides, 45 chains. Longest chain 18 peptides. Score 0.521 Round 3: 303 peptides, 43 chains. Longest chain 23 peptides. Score 0.549 Round 4: 320 peptides, 41 chains. Longest chain 20 peptides. Score 0.606 Round 5: 299 peptides, 43 chains. Longest chain 16 peptides. Score 0.539 Taking the results from Round 4 Chains 43, Residues 279, Estimated correctness of the model 42.7 % 7 chains (56 residues) have been docked in sequence ------------------------------------------------------ 9600 reflections ( 98.60 % complete ) and 9397 restraints for refining 4491 atoms. 8151 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2072 (Rfree = 0.000) for 4491 atoms. Found 40 (40 requested) and removed 40 (20 requested) atoms. Cycle 32: After refmac, R = 0.1799 (Rfree = 0.000) for 4479 atoms. Found 23 (40 requested) and removed 24 (20 requested) atoms. Cycle 33: After refmac, R = 0.1746 (Rfree = 0.000) for 4466 atoms. Found 18 (40 requested) and removed 21 (20 requested) atoms. Cycle 34: After refmac, R = 0.1741 (Rfree = 0.000) for 4459 atoms. Found 12 (40 requested) and removed 24 (20 requested) atoms. Cycle 35: After refmac, R = 0.1709 (Rfree = 0.000) for 4444 atoms. Found 11 (39 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.75 3.15 Search for helices and strands: 0 residues in 0 chains, 4532 seeds are put forward Round 1: 245 peptides, 44 chains. Longest chain 13 peptides. Score 0.386 Round 2: 279 peptides, 39 chains. Longest chain 17 peptides. Score 0.534 Round 3: 279 peptides, 39 chains. Longest chain 18 peptides. Score 0.534 Round 4: 292 peptides, 40 chains. Longest chain 23 peptides. Score 0.554 Round 5: 261 peptides, 39 chains. Longest chain 16 peptides. Score 0.489 Taking the results from Round 4 Chains 41, Residues 252, Estimated correctness of the model 28.1 % 6 chains (51 residues) have been docked in sequence ------------------------------------------------------ 9600 reflections ( 98.60 % complete ) and 9592 restraints for refining 4491 atoms. 8465 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1919 (Rfree = 0.000) for 4491 atoms. Found 25 (40 requested) and removed 31 (20 requested) atoms. Cycle 37: After refmac, R = 0.1797 (Rfree = 0.000) for 4481 atoms. Found 17 (40 requested) and removed 23 (20 requested) atoms. Cycle 38: After refmac, R = 0.1740 (Rfree = 0.000) for 4468 atoms. Found 21 (40 requested) and removed 20 (20 requested) atoms. Cycle 39: After refmac, R = 0.1682 (Rfree = 0.000) for 4469 atoms. Found 11 (40 requested) and removed 20 (20 requested) atoms. Cycle 40: After refmac, R = 0.1676 (Rfree = 0.000) for 4459 atoms. Found 17 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.75 3.15 Search for helices and strands: 0 residues in 0 chains, 4545 seeds are put forward Round 1: 258 peptides, 46 chains. Longest chain 16 peptides. Score 0.399 Round 2: 286 peptides, 40 chains. Longest chain 19 peptides. Score 0.540 Round 3: 282 peptides, 41 chains. Longest chain 16 peptides. Score 0.520 Round 4: 261 peptides, 41 chains. Longest chain 15 peptides. Score 0.466 Round 5: 269 peptides, 40 chains. Longest chain 17 peptides. Score 0.498 Taking the results from Round 2 Chains 43, Residues 246, Estimated correctness of the model 23.9 % 6 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9600 reflections ( 98.60 % complete ) and 9650 restraints for refining 4491 atoms. 8571 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1926 (Rfree = 0.000) for 4491 atoms. Found 17 (40 requested) and removed 27 (20 requested) atoms. Cycle 42: After refmac, R = 0.1837 (Rfree = 0.000) for 4474 atoms. Found 7 (40 requested) and removed 22 (20 requested) atoms. Cycle 43: After refmac, R = 0.1806 (Rfree = 0.000) for 4456 atoms. Found 17 (40 requested) and removed 20 (20 requested) atoms. Cycle 44: After refmac, R = 0.1756 (Rfree = 0.000) for 4451 atoms. Found 12 (39 requested) and removed 20 (19 requested) atoms. Cycle 45: After refmac, R = 0.1730 (Rfree = 0.000) for 4440 atoms. Found 7 (39 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.75 3.15 Search for helices and strands: 0 residues in 0 chains, 4508 seeds are put forward Round 1: 227 peptides, 40 chains. Longest chain 18 peptides. Score 0.384 Round 2: 252 peptides, 40 chains. Longest chain 19 peptides. Score 0.454 Round 3: 266 peptides, 42 chains. Longest chain 20 peptides. Score 0.468 Round 4: 259 peptides, 42 chains. Longest chain 15 peptides. Score 0.450 Round 5: 270 peptides, 40 chains. Longest chain 19 peptides. Score 0.501 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 230, Estimated correctness of the model 11.7 % 6 chains (44 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 1vk3-3_warpNtrace.pdb as input Building loops using Loopy2018 42 chains (230 residues) following loop building 6 chains (44 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9600 reflections ( 98.60 % complete ) and 9849 restraints for refining 4491 atoms. 8845 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2004 (Rfree = 0.000) for 4491 atoms. Found 0 (40 requested) and removed 18 (20 requested) atoms. Cycle 47: After refmac, R = 0.1880 (Rfree = 0.000) for 4467 atoms. Found 0 (40 requested) and removed 10 (20 requested) atoms. Cycle 48: After refmac, R = 0.1832 (Rfree = 0.000) for 4451 atoms. Found 0 (40 requested) and removed 3 (20 requested) atoms. Cycle 49: After refmac, R = 0.1800 (Rfree = 0.000) for 4448 atoms. Found 0 (39 requested) and removed 3 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:36:20 GMT 2018 Job finished. TimeTaking 68.4 Used memory is bytes: 13113392