null Sun 23 Dec 22:23:05 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 1vrb-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-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/1vrb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-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 ============================================================ Sun 23 Dec 22:23:15 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/1vrb-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-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 857 and 0 Target number of residues in the AU: 857 Target solvent content: 0.6729 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 10944 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: 48.979 4.000 Wilson plot Bfac: 94.96 12677 reflections ( 99.37 % complete ) and 0 restraints for refining 12106 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3559 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3408 (Rfree = 0.000) for 12106 atoms. Found 57 (57 requested) and removed 191 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.85 3.95 Search for helices and strands: 0 residues in 0 chains, 12217 seeds are put forward NCS extension: 0 residues added, 12217 seeds are put forward Round 1: 372 peptides, 75 chains. Longest chain 9 peptides. Score 0.271 Round 2: 478 peptides, 84 chains. Longest chain 13 peptides. Score 0.357 Round 3: 546 peptides, 90 chains. Longest chain 17 peptides. Score 0.407 Round 4: 556 peptides, 83 chains. Longest chain 17 peptides. Score 0.452 Round 5: 562 peptides, 83 chains. Longest chain 21 peptides. Score 0.458 Taking the results from Round 5 Chains 86, Residues 479, Estimated correctness of the model 0.0 % 7 chains (54 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 23746 restraints for refining 9875 atoms. 21749 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2830 (Rfree = 0.000) for 9875 atoms. Found 34 (46 requested) and removed 89 (23 requested) atoms. Cycle 2: After refmac, R = 0.2567 (Rfree = 0.000) for 9618 atoms. Found 43 (46 requested) and removed 63 (23 requested) atoms. Cycle 3: After refmac, R = 0.2108 (Rfree = 0.000) for 9468 atoms. Found 16 (45 requested) and removed 57 (22 requested) atoms. Cycle 4: After refmac, R = 0.2380 (Rfree = 0.000) for 9361 atoms. Found 44 (44 requested) and removed 46 (22 requested) atoms. Cycle 5: After refmac, R = 0.2338 (Rfree = 0.000) for 9313 atoms. Found 44 (44 requested) and removed 75 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 9545 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 9559 seeds are put forward Round 1: 466 peptides, 95 chains. Longest chain 13 peptides. Score 0.284 Round 2: 553 peptides, 95 chains. Longest chain 20 peptides. Score 0.390 Round 3: 561 peptides, 95 chains. Longest chain 14 peptides. Score 0.399 Round 4: 575 peptides, 89 chains. Longest chain 18 peptides. Score 0.444 Round 5: 563 peptides, 90 chains. Longest chain 15 peptides. Score 0.426 Taking the results from Round 4 Chains 90, Residues 486, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 21449 restraints for refining 9218 atoms. 19566 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2467 (Rfree = 0.000) for 9218 atoms. Found 43 (43 requested) and removed 93 (21 requested) atoms. Cycle 7: After refmac, R = 0.2416 (Rfree = 0.000) for 9084 atoms. Found 43 (43 requested) and removed 90 (21 requested) atoms. Cycle 8: After refmac, R = 0.2203 (Rfree = 0.000) for 8977 atoms. Found 42 (42 requested) and removed 77 (21 requested) atoms. Cycle 9: After refmac, R = 0.2149 (Rfree = 0.000) for 8905 atoms. Found 42 (42 requested) and removed 50 (21 requested) atoms. Cycle 10: After refmac, R = 0.2072 (Rfree = 0.000) for 8870 atoms. Found 42 (42 requested) and removed 51 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 9269 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 9291 seeds are put forward Round 1: 497 peptides, 102 chains. Longest chain 11 peptides. Score 0.286 Round 2: 590 peptides, 104 chains. Longest chain 15 peptides. Score 0.388 Round 3: 574 peptides, 91 chains. Longest chain 22 peptides. Score 0.433 Round 4: 581 peptides, 90 chains. Longest chain 17 peptides. Score 0.445 Round 5: 569 peptides, 86 chains. Longest chain 15 peptides. Score 0.452 Taking the results from Round 5 Chains 86, Residues 483, Estimated correctness of the model 0.0 % 7 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 21479 restraints for refining 9378 atoms. 19539 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2299 (Rfree = 0.000) for 9378 atoms. Found 42 (44 requested) and removed 130 (22 requested) atoms. Cycle 12: After refmac, R = 0.2090 (Rfree = 0.000) for 9220 atoms. Found 44 (44 requested) and removed 68 (22 requested) atoms. Cycle 13: After refmac, R = 0.1958 (Rfree = 0.000) for 9148 atoms. Found 37 (43 requested) and removed 58 (21 requested) atoms. Cycle 14: After refmac, R = 0.2109 (Rfree = 0.000) for 9087 atoms. Found 43 (43 requested) and removed 55 (21 requested) atoms. Cycle 15: After refmac, R = 0.1994 (Rfree = 0.000) for 9036 atoms. Found 36 (43 requested) and removed 51 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 3.88 Search for helices and strands: 0 residues in 0 chains, 9315 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 9330 seeds are put forward Round 1: 472 peptides, 95 chains. Longest chain 11 peptides. Score 0.292 Round 2: 551 peptides, 98 chains. Longest chain 11 peptides. Score 0.372 Round 3: 552 peptides, 92 chains. Longest chain 12 peptides. Score 0.404 Round 4: 550 peptides, 89 chains. Longest chain 13 peptides. Score 0.416 Round 5: 560 peptides, 89 chains. Longest chain 13 peptides. Score 0.427 Taking the results from Round 5 Chains 90, Residues 471, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 21803 restraints for refining 9464 atoms. 19948 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2375 (Rfree = 0.000) for 9464 atoms. Found 44 (44 requested) and removed 98 (22 requested) atoms. Cycle 17: After refmac, R = 0.2242 (Rfree = 0.000) for 9346 atoms. Found 44 (44 requested) and removed 71 (22 requested) atoms. Cycle 18: After refmac, R = 0.2150 (Rfree = 0.000) for 9270 atoms. Found 44 (44 requested) and removed 62 (22 requested) atoms. Cycle 19: After refmac, R = 0.2008 (Rfree = 0.000) for 9216 atoms. Found 43 (43 requested) and removed 47 (21 requested) atoms. Cycle 20: After refmac, R = 0.2075 (Rfree = 0.000) for 9188 atoms. Found 43 (43 requested) and removed 52 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.88 Search for helices and strands: 0 residues in 0 chains, 9478 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 9491 seeds are put forward Round 1: 485 peptides, 101 chains. Longest chain 10 peptides. Score 0.276 Round 2: 560 peptides, 99 chains. Longest chain 13 peptides. Score 0.378 Round 3: 535 peptides, 90 chains. Longest chain 13 peptides. Score 0.394 Round 4: 540 peptides, 85 chains. Longest chain 15 peptides. Score 0.425 Round 5: 545 peptides, 85 chains. Longest chain 17 peptides. Score 0.430 Taking the results from Round 5 Chains 85, Residues 460, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 22439 restraints for refining 9583 atoms. 20684 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2372 (Rfree = 0.000) for 9583 atoms. Found 45 (45 requested) and removed 93 (22 requested) atoms. Cycle 22: After refmac, R = 0.2116 (Rfree = 0.000) for 9482 atoms. Found 45 (45 requested) and removed 62 (22 requested) atoms. Cycle 23: After refmac, R = 0.2147 (Rfree = 0.000) for 9436 atoms. Found 44 (44 requested) and removed 61 (22 requested) atoms. Cycle 24: After refmac, R = 0.2014 (Rfree = 0.000) for 9387 atoms. Found 37 (44 requested) and removed 44 (22 requested) atoms. Cycle 25: After refmac, R = 0.1673 (Rfree = 0.000) for 9344 atoms. Found 9 (44 requested) and removed 39 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 3.91 Search for helices and strands: 0 residues in 0 chains, 9582 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 9612 seeds are put forward Round 1: 445 peptides, 96 chains. Longest chain 9 peptides. Score 0.251 Round 2: 506 peptides, 90 chains. Longest chain 16 peptides. Score 0.360 Round 3: 515 peptides, 94 chains. Longest chain 10 peptides. Score 0.350 Round 4: 527 peptides, 91 chains. Longest chain 13 peptides. Score 0.380 Round 5: 532 peptides, 85 chains. Longest chain 15 peptides. Score 0.416 Taking the results from Round 5 Chains 85, Residues 447, Estimated correctness of the model 0.0 % 6 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 23026 restraints for refining 9786 atoms. 21248 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2363 (Rfree = 0.000) for 9786 atoms. Found 39 (46 requested) and removed 88 (23 requested) atoms. Cycle 27: After refmac, R = 0.2218 (Rfree = 0.000) for 9659 atoms. Found 46 (46 requested) and removed 101 (23 requested) atoms. Cycle 28: After refmac, R = 0.2105 (Rfree = 0.000) for 9557 atoms. Found 45 (45 requested) and removed 71 (22 requested) atoms. Cycle 29: After refmac, R = 0.2225 (Rfree = 0.000) for 9475 atoms. Found 45 (45 requested) and removed 64 (22 requested) atoms. Cycle 30: After refmac, R = 0.2182 (Rfree = 0.000) for 9433 atoms. Found 44 (44 requested) and removed 64 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.90 Search for helices and strands: 0 residues in 0 chains, 9679 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 9706 seeds are put forward Round 1: 386 peptides, 80 chains. Longest chain 10 peptides. Score 0.262 Round 2: 431 peptides, 79 chains. Longest chain 13 peptides. Score 0.326 Round 3: 440 peptides, 79 chains. Longest chain 14 peptides. Score 0.337 Round 4: 457 peptides, 78 chains. Longest chain 14 peptides. Score 0.364 Round 5: 456 peptides, 79 chains. Longest chain 14 peptides. Score 0.357 Taking the results from Round 4 Chains 78, Residues 379, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 22514 restraints for refining 9533 atoms. 21069 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2269 (Rfree = 0.000) for 9533 atoms. Found 45 (45 requested) and removed 66 (22 requested) atoms. Cycle 32: After refmac, R = 0.2238 (Rfree = 0.000) for 9460 atoms. Found 45 (45 requested) and removed 69 (22 requested) atoms. Cycle 33: After refmac, R = 0.2030 (Rfree = 0.000) for 9409 atoms. Found 44 (44 requested) and removed 52 (22 requested) atoms. Cycle 34: After refmac, R = 0.2134 (Rfree = 0.000) for 9376 atoms. Found 44 (44 requested) and removed 42 (22 requested) atoms. Cycle 35: After refmac, R = 0.2188 (Rfree = 0.000) for 9349 atoms. Found 44 (44 requested) and removed 38 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 3.91 Search for helices and strands: 0 residues in 0 chains, 9609 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 9622 seeds are put forward Round 1: 359 peptides, 81 chains. Longest chain 7 peptides. Score 0.218 Round 2: 448 peptides, 92 chains. Longest chain 8 peptides. Score 0.277 Round 3: 451 peptides, 89 chains. Longest chain 10 peptides. Score 0.297 Round 4: 435 peptides, 81 chains. Longest chain 10 peptides. Score 0.320 Round 5: 432 peptides, 81 chains. Longest chain 10 peptides. Score 0.317 Taking the results from Round 4 Chains 81, Residues 354, Estimated correctness of the model 0.0 % 5 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 22488 restraints for refining 9570 atoms. 21107 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2324 (Rfree = 0.000) for 9570 atoms. Found 45 (45 requested) and removed 84 (22 requested) atoms. Cycle 37: After refmac, R = 0.2175 (Rfree = 0.000) for 9486 atoms. Found 45 (45 requested) and removed 56 (22 requested) atoms. Cycle 38: After refmac, R = 0.2061 (Rfree = 0.000) for 9446 atoms. Found 42 (45 requested) and removed 55 (22 requested) atoms. Cycle 39: After refmac, R = 0.1704 (Rfree = 0.000) for 9417 atoms. Found 12 (44 requested) and removed 35 (22 requested) atoms. Cycle 40: After refmac, R = 0.1648 (Rfree = 0.000) for 9376 atoms. Found 7 (44 requested) and removed 32 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.92 Search for helices and strands: 0 residues in 0 chains, 9587 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 9599 seeds are put forward Round 1: 347 peptides, 75 chains. Longest chain 8 peptides. Score 0.237 Round 2: 371 peptides, 69 chains. Longest chain 13 peptides. Score 0.305 Round 3: 382 peptides, 69 chains. Longest chain 11 peptides. Score 0.319 Round 4: 392 peptides, 71 chains. Longest chain 10 peptides. Score 0.321 Round 5: 406 peptides, 69 chains. Longest chain 15 peptides. Score 0.350 Taking the results from Round 5 Chains 70, Residues 337, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 22175 restraints for refining 9488 atoms. 20808 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2173 (Rfree = 0.000) for 9488 atoms. Found 45 (45 requested) and removed 68 (22 requested) atoms. Cycle 42: After refmac, R = 0.2165 (Rfree = 0.000) for 9432 atoms. Found 44 (44 requested) and removed 55 (22 requested) atoms. Cycle 43: After refmac, R = 0.2075 (Rfree = 0.000) for 9393 atoms. Found 44 (44 requested) and removed 44 (22 requested) atoms. Cycle 44: After refmac, R = 0.2148 (Rfree = 0.000) for 9367 atoms. Found 44 (44 requested) and removed 47 (22 requested) atoms. Cycle 45: After refmac, R = 0.1762 (Rfree = 0.000) for 9339 atoms. Found 13 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.93 Search for helices and strands: 0 residues in 0 chains, 9585 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 9604 seeds are put forward Round 1: 306 peptides, 69 chains. Longest chain 8 peptides. Score 0.213 Round 2: 372 peptides, 74 chains. Longest chain 10 peptides. Score 0.277 Round 3: 335 peptides, 66 chains. Longest chain 10 peptides. Score 0.273 Round 4: 353 peptides, 68 chains. Longest chain 14 peptides. Score 0.286 Round 5: 347 peptides, 63 chains. Longest chain 14 peptides. Score 0.308 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 284, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vrb-4_warpNtrace.pdb as input Building loops using Loopy2018 63 chains (284 residues) following loop building 3 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12677 reflections ( 99.37 % complete ) and 22505 restraints for refining 9373 atoms. 21418 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2440 (Rfree = 0.000) for 9373 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2374 (Rfree = 0.000) for 9312 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2302 (Rfree = 0.000) for 9268 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.2264 (Rfree = 0.000) for 9221 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:12:15 GMT 2018 Job finished. TimeTaking 109.17 Used memory is bytes: 7665200