null Mon 24 Dec 08:01:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vky-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vky-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vky-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.2-parrot-noncs ############### 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 08:01:12 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/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vky-3.2-parrot-noncs/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 759 and 0 Target number of residues in the AU: 759 Target solvent content: 0.5743 Checking the provided sequence file Detected sequence length: 347 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 694 Adjusted target solvent content: 0.61 Input MTZ file: 1vky-3.2-parrot-noncs.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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 5552 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: 41.380 3.200 Wilson plot Bfac: 43.08 16292 reflections ( 99.71 % complete ) and 0 restraints for refining 6207 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3203 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2320 (Rfree = 0.000) for 6207 atoms. Found 37 (55 requested) and removed 84 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.88 2.48 Search for helices and strands: 0 residues in 0 chains, 6276 seeds are put forward NCS extension: 0 residues added, 6276 seeds are put forward Round 1: 351 peptides, 57 chains. Longest chain 15 peptides. Score 0.403 Round 2: 405 peptides, 57 chains. Longest chain 23 peptides. Score 0.490 Round 3: 399 peptides, 48 chains. Longest chain 36 peptides. Score 0.541 Round 4: 427 peptides, 48 chains. Longest chain 39 peptides. Score 0.579 Round 5: 438 peptides, 53 chains. Longest chain 28 peptides. Score 0.563 Taking the results from Round 4 Chains 51, Residues 379, Estimated correctness of the model 35.3 % 4 chains (75 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10120 restraints for refining 5068 atoms. 8332 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2641 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 45 (22 requested) atoms. Cycle 2: After refmac, R = 0.2452 (Rfree = 0.000) for 5038 atoms. Found 30 (45 requested) and removed 34 (22 requested) atoms. Cycle 3: After refmac, R = 0.2354 (Rfree = 0.000) for 5018 atoms. Found 19 (45 requested) and removed 26 (22 requested) atoms. Cycle 4: After refmac, R = 0.2339 (Rfree = 0.000) for 5004 atoms. Found 18 (44 requested) and removed 27 (22 requested) atoms. Cycle 5: After refmac, R = 0.2291 (Rfree = 0.000) for 4984 atoms. Found 22 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.88 2.48 Search for helices and strands: 0 residues in 0 chains, 5125 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 5158 seeds are put forward Round 1: 392 peptides, 48 chains. Longest chain 33 peptides. Score 0.531 Round 2: 425 peptides, 48 chains. Longest chain 37 peptides. Score 0.576 Round 3: 429 peptides, 51 chains. Longest chain 24 peptides. Score 0.563 Round 4: 411 peptides, 44 chains. Longest chain 30 peptides. Score 0.583 Round 5: 419 peptides, 49 chains. Longest chain 24 peptides. Score 0.562 Taking the results from Round 4 Chains 44, Residues 367, Estimated correctness of the model 36.4 % 4 chains (74 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10256 restraints for refining 5068 atoms. 8494 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2678 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 44 (22 requested) atoms. Cycle 7: After refmac, R = 0.2458 (Rfree = 0.000) for 5051 atoms. Found 30 (45 requested) and removed 36 (22 requested) atoms. Cycle 8: After refmac, R = 0.2371 (Rfree = 0.000) for 5031 atoms. Found 13 (45 requested) and removed 24 (22 requested) atoms. Cycle 9: After refmac, R = 0.2335 (Rfree = 0.000) for 5011 atoms. Found 17 (45 requested) and removed 23 (22 requested) atoms. Cycle 10: After refmac, R = 0.2306 (Rfree = 0.000) for 4999 atoms. Found 19 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.92 2.52 Search for helices and strands: 0 residues in 0 chains, 5091 seeds are put forward NCS extension: 49 residues added (7 deleted due to clashes), 5140 seeds are put forward Round 1: 390 peptides, 54 chains. Longest chain 16 peptides. Score 0.487 Round 2: 425 peptides, 48 chains. Longest chain 37 peptides. Score 0.576 Round 3: 430 peptides, 45 chains. Longest chain 35 peptides. Score 0.601 Round 4: 442 peptides, 49 chains. Longest chain 49 peptides. Score 0.592 Round 5: 440 peptides, 46 chains. Longest chain 51 peptides. Score 0.608 Taking the results from Round 5 Chains 49, Residues 394, Estimated correctness of the model 43.2 % 5 chains (114 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9473 restraints for refining 5067 atoms. 7450 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2764 (Rfree = 0.000) for 5067 atoms. Found 45 (45 requested) and removed 34 (22 requested) atoms. Cycle 12: After refmac, R = 0.2568 (Rfree = 0.000) for 5053 atoms. Found 37 (45 requested) and removed 27 (22 requested) atoms. Cycle 13: After refmac, R = 0.2460 (Rfree = 0.000) for 5052 atoms. Found 21 (45 requested) and removed 23 (22 requested) atoms. Cycle 14: After refmac, R = 0.2394 (Rfree = 0.000) for 5040 atoms. Found 10 (45 requested) and removed 23 (22 requested) atoms. Cycle 15: After refmac, R = 0.2354 (Rfree = 0.000) for 5020 atoms. Found 16 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.91 2.51 Search for helices and strands: 0 residues in 0 chains, 5129 seeds are put forward NCS extension: 34 residues added (18 deleted due to clashes), 5163 seeds are put forward Round 1: 395 peptides, 51 chains. Longest chain 44 peptides. Score 0.515 Round 2: 430 peptides, 49 chains. Longest chain 28 peptides. Score 0.577 Round 3: 420 peptides, 47 chains. Longest chain 37 peptides. Score 0.576 Round 4: 434 peptides, 50 chains. Longest chain 24 peptides. Score 0.576 Round 5: 433 peptides, 46 chains. Longest chain 38 peptides. Score 0.599 Taking the results from Round 5 Chains 47, Residues 387, Estimated correctness of the model 40.8 % 5 chains (75 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10114 restraints for refining 5067 atoms. 8307 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2646 (Rfree = 0.000) for 5067 atoms. Found 45 (45 requested) and removed 33 (22 requested) atoms. Cycle 17: After refmac, R = 0.2443 (Rfree = 0.000) for 5065 atoms. Found 26 (45 requested) and removed 27 (22 requested) atoms. Cycle 18: After refmac, R = 0.2374 (Rfree = 0.000) for 5049 atoms. Found 23 (45 requested) and removed 23 (22 requested) atoms. Cycle 19: After refmac, R = 0.2324 (Rfree = 0.000) for 5041 atoms. Found 20 (45 requested) and removed 22 (22 requested) atoms. Cycle 20: After refmac, R = 0.2334 (Rfree = 0.000) for 5032 atoms. Found 21 (45 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.94 2.53 Search for helices and strands: 0 residues in 0 chains, 5127 seeds are put forward NCS extension: 34 residues added (11 deleted due to clashes), 5161 seeds are put forward Round 1: 407 peptides, 55 chains. Longest chain 27 peptides. Score 0.506 Round 2: 441 peptides, 50 chains. Longest chain 27 peptides. Score 0.585 Round 3: 433 peptides, 49 chains. Longest chain 26 peptides. Score 0.581 Round 4: 436 peptides, 51 chains. Longest chain 25 peptides. Score 0.572 Round 5: 425 peptides, 50 chains. Longest chain 24 peptides. Score 0.564 Taking the results from Round 2 Chains 54, Residues 391, Estimated correctness of the model 37.0 % 8 chains (113 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9594 restraints for refining 5067 atoms. 7604 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2631 (Rfree = 0.000) for 5067 atoms. Found 45 (45 requested) and removed 35 (22 requested) atoms. Cycle 22: After refmac, R = 0.2485 (Rfree = 0.000) for 5058 atoms. Found 38 (45 requested) and removed 29 (22 requested) atoms. Cycle 23: After refmac, R = 0.2420 (Rfree = 0.000) for 5062 atoms. Found 18 (45 requested) and removed 24 (22 requested) atoms. Cycle 24: After refmac, R = 0.2370 (Rfree = 0.000) for 5048 atoms. Found 12 (45 requested) and removed 26 (22 requested) atoms. Cycle 25: After refmac, R = 0.2337 (Rfree = 0.000) for 5031 atoms. Found 18 (45 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.91 2.51 Search for helices and strands: 0 residues in 0 chains, 5120 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 5147 seeds are put forward Round 1: 379 peptides, 52 chains. Longest chain 19 peptides. Score 0.484 Round 2: 404 peptides, 48 chains. Longest chain 34 peptides. Score 0.548 Round 3: 401 peptides, 45 chains. Longest chain 20 peptides. Score 0.563 Round 4: 408 peptides, 49 chains. Longest chain 24 peptides. Score 0.547 Round 5: 414 peptides, 48 chains. Longest chain 30 peptides. Score 0.561 Taking the results from Round 3 Chains 47, Residues 356, Estimated correctness of the model 30.7 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10538 restraints for refining 5067 atoms. 8925 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2567 (Rfree = 0.000) for 5067 atoms. Found 45 (45 requested) and removed 26 (22 requested) atoms. Cycle 27: After refmac, R = 0.2394 (Rfree = 0.000) for 5064 atoms. Found 24 (45 requested) and removed 27 (22 requested) atoms. Cycle 28: After refmac, R = 0.2320 (Rfree = 0.000) for 5050 atoms. Found 15 (45 requested) and removed 25 (22 requested) atoms. Cycle 29: After refmac, R = 0.2266 (Rfree = 0.000) for 5036 atoms. Found 13 (45 requested) and removed 24 (22 requested) atoms. Cycle 30: After refmac, R = 0.2246 (Rfree = 0.000) for 5019 atoms. Found 17 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.88 2.48 Search for helices and strands: 0 residues in 0 chains, 5128 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 5166 seeds are put forward Round 1: 353 peptides, 50 chains. Longest chain 21 peptides. Score 0.458 Round 2: 388 peptides, 47 chains. Longest chain 38 peptides. Score 0.532 Round 3: 408 peptides, 47 chains. Longest chain 42 peptides. Score 0.560 Round 4: 395 peptides, 45 chains. Longest chain 37 peptides. Score 0.555 Round 5: 412 peptides, 49 chains. Longest chain 39 peptides. Score 0.552 Taking the results from Round 3 Chains 48, Residues 361, Estimated correctness of the model 29.8 % 3 chains (68 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10121 restraints for refining 5068 atoms. 8402 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2574 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 34 (22 requested) atoms. Cycle 32: After refmac, R = 0.2438 (Rfree = 0.000) for 5058 atoms. Found 36 (45 requested) and removed 28 (22 requested) atoms. Cycle 33: After refmac, R = 0.2377 (Rfree = 0.000) for 5048 atoms. Found 24 (45 requested) and removed 24 (22 requested) atoms. Cycle 34: After refmac, R = 0.2340 (Rfree = 0.000) for 5044 atoms. Found 12 (45 requested) and removed 23 (22 requested) atoms. Cycle 35: After refmac, R = 0.2340 (Rfree = 0.000) for 5027 atoms. Found 17 (45 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.90 2.50 Search for helices and strands: 0 residues in 0 chains, 5104 seeds are put forward NCS extension: 35 residues added (27 deleted due to clashes), 5139 seeds are put forward Round 1: 371 peptides, 48 chains. Longest chain 23 peptides. Score 0.500 Round 2: 416 peptides, 48 chains. Longest chain 22 peptides. Score 0.564 Round 3: 399 peptides, 45 chains. Longest chain 21 peptides. Score 0.560 Round 4: 414 peptides, 43 chains. Longest chain 23 peptides. Score 0.593 Round 5: 410 peptides, 43 chains. Longest chain 34 peptides. Score 0.587 Taking the results from Round 4 Chains 46, Residues 371, Estimated correctness of the model 39.2 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10507 restraints for refining 5067 atoms. 8871 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2502 (Rfree = 0.000) for 5067 atoms. Found 41 (45 requested) and removed 35 (22 requested) atoms. Cycle 37: After refmac, R = 0.2345 (Rfree = 0.000) for 5052 atoms. Found 22 (45 requested) and removed 30 (22 requested) atoms. Cycle 38: After refmac, R = 0.2338 (Rfree = 0.000) for 5040 atoms. Found 15 (45 requested) and removed 26 (22 requested) atoms. Cycle 39: After refmac, R = 0.2266 (Rfree = 0.000) for 5025 atoms. Found 12 (45 requested) and removed 23 (22 requested) atoms. Cycle 40: After refmac, R = 0.2282 (Rfree = 0.000) for 5010 atoms. Found 14 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.87 2.47 Search for helices and strands: 0 residues in 0 chains, 5121 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 5132 seeds are put forward Round 1: 388 peptides, 53 chains. Longest chain 19 peptides. Score 0.491 Round 2: 405 peptides, 48 chains. Longest chain 20 peptides. Score 0.549 Round 3: 403 peptides, 47 chains. Longest chain 27 peptides. Score 0.553 Round 4: 407 peptides, 44 chains. Longest chain 30 peptides. Score 0.577 Round 5: 382 peptides, 45 chains. Longest chain 22 peptides. Score 0.536 Taking the results from Round 4 Chains 46, Residues 363, Estimated correctness of the model 34.7 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10329 restraints for refining 5068 atoms. 8668 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2534 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 32 (22 requested) atoms. Cycle 42: After refmac, R = 0.2346 (Rfree = 0.000) for 5070 atoms. Found 18 (45 requested) and removed 26 (22 requested) atoms. Cycle 43: After refmac, R = 0.2268 (Rfree = 0.000) for 5047 atoms. Found 21 (45 requested) and removed 23 (22 requested) atoms. Cycle 44: After refmac, R = 0.2246 (Rfree = 0.000) for 5039 atoms. Found 20 (45 requested) and removed 23 (22 requested) atoms. Cycle 45: After refmac, R = 0.2231 (Rfree = 0.000) for 5031 atoms. Found 14 (45 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.87 2.47 Search for helices and strands: 0 residues in 0 chains, 5120 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 5138 seeds are put forward Round 1: 391 peptides, 53 chains. Longest chain 20 peptides. Score 0.496 Round 2: 414 peptides, 49 chains. Longest chain 22 peptides. Score 0.555 Round 3: 413 peptides, 51 chains. Longest chain 24 peptides. Score 0.541 Round 4: 408 peptides, 49 chains. Longest chain 25 peptides. Score 0.547 Round 5: 409 peptides, 53 chains. Longest chain 26 peptides. Score 0.522 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 365, Estimated correctness of the model 28.4 % 4 chains (73 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 50 chains (365 residues) following loop building 4 chains (73 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16292 reflections ( 99.71 % complete ) and 9951 restraints for refining 5068 atoms. 8211 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2491 (Rfree = 0.000) for 5068 atoms. Found 0 (45 requested) and removed 12 (22 requested) atoms. Cycle 47: After refmac, R = 0.2409 (Rfree = 0.000) for 5041 atoms. Found 0 (45 requested) and removed 9 (22 requested) atoms. Cycle 48: After refmac, R = 0.2376 (Rfree = 0.000) for 5027 atoms. Found 0 (45 requested) and removed 5 (22 requested) atoms. Cycle 49: After refmac, R = 0.2366 (Rfree = 0.000) for 5019 atoms. Found 0 (45 requested) and removed 1 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:02:34 GMT 2018 Job finished. TimeTaking 61.44 Used memory is bytes: 18222608