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 2gvh-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-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/2gvh-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-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/2gvh-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-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 723 and 0 Target number of residues in the AU: 723 Target solvent content: 0.6746 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.85 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: 121.211 3.600 Wilson plot Bfac: 96.24 13898 reflections ( 99.67 % complete ) and 0 restraints for refining 7620 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3594 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3214 (Rfree = 0.000) for 7620 atoms. Found 48 (48 requested) and removed 86 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.25 Search for helices and strands: 0 residues in 0 chains, 7658 seeds are put forward NCS extension: 0 residues added, 7658 seeds are put forward Round 1: 382 peptides, 73 chains. Longest chain 14 peptides. Score 0.312 Round 2: 433 peptides, 68 chains. Longest chain 16 peptides. Score 0.415 Round 3: 424 peptides, 62 chains. Longest chain 17 peptides. Score 0.439 Round 4: 450 peptides, 66 chains. Longest chain 21 peptides. Score 0.450 Round 5: 458 peptides, 62 chains. Longest chain 21 peptides. Score 0.482 Taking the results from Round 5 Chains 65, Residues 396, Estimated correctness of the model 0.0 % 5 chains (49 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14081 restraints for refining 6265 atoms. 12377 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2566 (Rfree = 0.000) for 6265 atoms. Found 26 (40 requested) and removed 29 (20 requested) atoms. Cycle 2: After refmac, R = 0.2353 (Rfree = 0.000) for 6162 atoms. Found 17 (40 requested) and removed 32 (20 requested) atoms. Cycle 3: After refmac, R = 0.2292 (Rfree = 0.000) for 6118 atoms. Found 10 (39 requested) and removed 33 (19 requested) atoms. Cycle 4: After refmac, R = 0.2333 (Rfree = 0.000) for 6078 atoms. Found 8 (39 requested) and removed 23 (19 requested) atoms. Cycle 5: After refmac, R = 0.2285 (Rfree = 0.000) for 6048 atoms. Found 11 (38 requested) and removed 31 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.17 Search for helices and strands: 0 residues in 0 chains, 6168 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 6186 seeds are put forward Round 1: 408 peptides, 70 chains. Longest chain 19 peptides. Score 0.369 Round 2: 454 peptides, 68 chains. Longest chain 23 peptides. Score 0.443 Round 3: 450 peptides, 65 chains. Longest chain 26 peptides. Score 0.455 Round 4: 461 peptides, 66 chains. Longest chain 25 peptides. Score 0.464 Round 5: 460 peptides, 68 chains. Longest chain 28 peptides. Score 0.451 Taking the results from Round 4 Chains 67, Residues 395, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14413 restraints for refining 6264 atoms. 12842 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2493 (Rfree = 0.000) for 6264 atoms. Found 38 (40 requested) and removed 36 (20 requested) atoms. Cycle 7: After refmac, R = 0.2309 (Rfree = 0.000) for 6238 atoms. Found 29 (40 requested) and removed 34 (20 requested) atoms. Cycle 8: After refmac, R = 0.2214 (Rfree = 0.000) for 6209 atoms. Found 8 (39 requested) and removed 29 (19 requested) atoms. Cycle 9: After refmac, R = 0.2629 (Rfree = 0.000) for 6178 atoms. Found 39 (39 requested) and removed 52 (19 requested) atoms. Cycle 10: After refmac, R = 0.2184 (Rfree = 0.000) for 6145 atoms. Found 29 (39 requested) and removed 39 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.19 Search for helices and strands: 0 residues in 0 chains, 6367 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 6386 seeds are put forward Round 1: 414 peptides, 74 chains. Longest chain 21 peptides. Score 0.353 Round 2: 460 peptides, 71 chains. Longest chain 19 peptides. Score 0.434 Round 3: 478 peptides, 71 chains. Longest chain 25 peptides. Score 0.457 Round 4: 468 peptides, 65 chains. Longest chain 19 peptides. Score 0.478 Round 5: 491 peptides, 71 chains. Longest chain 15 peptides. Score 0.473 Taking the results from Round 4 Chains 68, Residues 403, Estimated correctness of the model 0.0 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 13893 restraints for refining 6266 atoms. 12179 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2283 (Rfree = 0.000) for 6266 atoms. Found 33 (40 requested) and removed 44 (20 requested) atoms. Cycle 12: After refmac, R = 0.2149 (Rfree = 0.000) for 6214 atoms. Found 11 (40 requested) and removed 26 (20 requested) atoms. Cycle 13: After refmac, R = 0.2119 (Rfree = 0.000) for 6189 atoms. Found 5 (39 requested) and removed 28 (19 requested) atoms. Cycle 14: After refmac, R = 0.2088 (Rfree = 0.000) for 6163 atoms. Found 10 (39 requested) and removed 25 (19 requested) atoms. Cycle 15: After refmac, R = 0.2142 (Rfree = 0.000) for 6143 atoms. Found 8 (39 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.20 Search for helices and strands: 0 residues in 0 chains, 6317 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 6343 seeds are put forward Round 1: 406 peptides, 70 chains. Longest chain 18 peptides. Score 0.366 Round 2: 446 peptides, 64 chains. Longest chain 22 peptides. Score 0.456 Round 3: 448 peptides, 61 chains. Longest chain 19 peptides. Score 0.476 Round 4: 459 peptides, 66 chains. Longest chain 19 peptides. Score 0.461 Round 5: 457 peptides, 64 chains. Longest chain 19 peptides. Score 0.470 Taking the results from Round 3 Chains 62, Residues 387, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14343 restraints for refining 6264 atoms. 12734 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2366 (Rfree = 0.000) for 6264 atoms. Found 30 (40 requested) and removed 32 (20 requested) atoms. Cycle 17: After refmac, R = 0.2214 (Rfree = 0.000) for 6220 atoms. Found 10 (40 requested) and removed 29 (20 requested) atoms. Cycle 18: After refmac, R = 0.2190 (Rfree = 0.000) for 6183 atoms. Found 9 (39 requested) and removed 27 (19 requested) atoms. Cycle 19: After refmac, R = 0.2121 (Rfree = 0.000) for 6161 atoms. Found 6 (39 requested) and removed 23 (19 requested) atoms. Cycle 20: After refmac, R = 0.2098 (Rfree = 0.000) for 6138 atoms. Found 4 (39 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.18 Search for helices and strands: 0 residues in 0 chains, 6298 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6321 seeds are put forward Round 1: 401 peptides, 68 chains. Longest chain 18 peptides. Score 0.371 Round 2: 455 peptides, 70 chains. Longest chain 15 peptides. Score 0.433 Round 3: 442 peptides, 62 chains. Longest chain 25 peptides. Score 0.462 Round 4: 467 peptides, 69 chains. Longest chain 23 peptides. Score 0.454 Round 5: 449 peptides, 58 chains. Longest chain 20 peptides. Score 0.494 Taking the results from Round 5 Chains 61, Residues 391, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14478 restraints for refining 6264 atoms. 12913 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2353 (Rfree = 0.000) for 6264 atoms. Found 33 (40 requested) and removed 32 (20 requested) atoms. Cycle 22: After refmac, R = 0.2263 (Rfree = 0.000) for 6232 atoms. Found 10 (40 requested) and removed 23 (20 requested) atoms. Cycle 23: After refmac, R = 0.2234 (Rfree = 0.000) for 6209 atoms. Found 9 (39 requested) and removed 22 (19 requested) atoms. Cycle 24: After refmac, R = 0.2448 (Rfree = 0.000) for 6191 atoms. Found 39 (39 requested) and removed 33 (19 requested) atoms. Cycle 25: After refmac, R = 0.2303 (Rfree = 0.000) for 6188 atoms. Found 16 (39 requested) and removed 38 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.19 Search for helices and strands: 0 residues in 0 chains, 6333 seeds are put forward NCS extension: 38 residues added (3 deleted due to clashes), 6371 seeds are put forward Round 1: 372 peptides, 69 chains. Longest chain 16 peptides. Score 0.323 Round 2: 443 peptides, 65 chains. Longest chain 22 peptides. Score 0.446 Round 3: 430 peptides, 61 chains. Longest chain 22 peptides. Score 0.453 Round 4: 431 peptides, 61 chains. Longest chain 26 peptides. Score 0.454 Round 5: 429 peptides, 60 chains. Longest chain 22 peptides. Score 0.457 Taking the results from Round 5 Chains 61, Residues 369, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14675 restraints for refining 6266 atoms. 13194 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2385 (Rfree = 0.000) for 6266 atoms. Found 29 (40 requested) and removed 27 (20 requested) atoms. Cycle 27: After refmac, R = 0.2284 (Rfree = 0.000) for 6241 atoms. Found 14 (40 requested) and removed 25 (20 requested) atoms. Cycle 28: After refmac, R = 0.2248 (Rfree = 0.000) for 6222 atoms. Found 10 (39 requested) and removed 20 (19 requested) atoms. Cycle 29: After refmac, R = 0.2240 (Rfree = 0.000) for 6209 atoms. Found 5 (39 requested) and removed 21 (19 requested) atoms. Cycle 30: After refmac, R = 0.2227 (Rfree = 0.000) for 6189 atoms. Found 7 (39 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.21 Search for helices and strands: 0 residues in 0 chains, 6309 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 6338 seeds are put forward Round 1: 360 peptides, 61 chains. Longest chain 13 peptides. Score 0.357 Round 2: 410 peptides, 61 chains. Longest chain 15 peptides. Score 0.426 Round 3: 408 peptides, 58 chains. Longest chain 27 peptides. Score 0.442 Round 4: 415 peptides, 55 chains. Longest chain 20 peptides. Score 0.468 Round 5: 421 peptides, 61 chains. Longest chain 38 peptides. Score 0.441 Taking the results from Round 4 Chains 55, Residues 360, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14860 restraints for refining 6265 atoms. 13475 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2294 (Rfree = 0.000) for 6265 atoms. Found 20 (40 requested) and removed 31 (20 requested) atoms. Cycle 32: After refmac, R = 0.2252 (Rfree = 0.000) for 6234 atoms. Found 12 (40 requested) and removed 29 (20 requested) atoms. Cycle 33: After refmac, R = 0.2389 (Rfree = 0.000) for 6207 atoms. Found 16 (39 requested) and removed 40 (19 requested) atoms. Cycle 34: After refmac, R = 0.2453 (Rfree = 0.000) for 6179 atoms. Found 25 (39 requested) and removed 26 (19 requested) atoms. Cycle 35: After refmac, R = 0.2444 (Rfree = 0.000) for 6175 atoms. Found 18 (39 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.18 Search for helices and strands: 0 residues in 0 chains, 6353 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6374 seeds are put forward Round 1: 342 peptides, 68 chains. Longest chain 10 peptides. Score 0.284 Round 2: 380 peptides, 61 chains. Longest chain 16 peptides. Score 0.385 Round 3: 383 peptides, 59 chains. Longest chain 20 peptides. Score 0.402 Round 4: 363 peptides, 54 chains. Longest chain 20 peptides. Score 0.406 Round 5: 369 peptides, 53 chains. Longest chain 17 peptides. Score 0.420 Taking the results from Round 5 Chains 54, Residues 316, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 15081 restraints for refining 6266 atoms. 13789 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2563 (Rfree = 0.000) for 6266 atoms. Found 38 (40 requested) and removed 30 (20 requested) atoms. Cycle 37: After refmac, R = 0.2425 (Rfree = 0.000) for 6252 atoms. Found 9 (40 requested) and removed 33 (20 requested) atoms. Cycle 38: After refmac, R = 0.2435 (Rfree = 0.000) for 6214 atoms. Found 22 (39 requested) and removed 31 (19 requested) atoms. Cycle 39: After refmac, R = 0.2397 (Rfree = 0.000) for 6204 atoms. Found 20 (39 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.2372 (Rfree = 0.000) for 6196 atoms. Found 23 (39 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.20 Search for helices and strands: 0 residues in 0 chains, 6333 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6352 seeds are put forward Round 1: 311 peptides, 59 chains. Longest chain 16 peptides. Score 0.296 Round 2: 373 peptides, 61 chains. Longest chain 14 peptides. Score 0.376 Round 3: 368 peptides, 57 chains. Longest chain 15 peptides. Score 0.394 Round 4: 349 peptides, 54 chains. Longest chain 15 peptides. Score 0.386 Round 5: 376 peptides, 58 chains. Longest chain 19 peptides. Score 0.399 Taking the results from Round 5 Chains 58, Residues 318, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 15119 restraints for refining 6266 atoms. 13905 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2540 (Rfree = 0.000) for 6266 atoms. Found 35 (40 requested) and removed 27 (20 requested) atoms. Cycle 42: After refmac, R = 0.2530 (Rfree = 0.000) for 6243 atoms. Found 35 (40 requested) and removed 27 (20 requested) atoms. Cycle 43: After refmac, R = 0.2401 (Rfree = 0.000) for 6237 atoms. Found 20 (40 requested) and removed 26 (20 requested) atoms. Cycle 44: After refmac, R = 0.2437 (Rfree = 0.000) for 6223 atoms. Found 32 (39 requested) and removed 28 (19 requested) atoms. Cycle 45: After refmac, R = 0.2372 (Rfree = 0.000) for 6220 atoms. Found 29 (39 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.17 Search for helices and strands: 0 residues in 0 chains, 6393 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6411 seeds are put forward Round 1: 283 peptides, 60 chains. Longest chain 9 peptides. Score 0.243 Round 2: 337 peptides, 60 chains. Longest chain 15 peptides. Score 0.329 Round 3: 354 peptides, 57 chains. Longest chain 20 peptides. Score 0.374 Round 4: 352 peptides, 58 chains. Longest chain 15 peptides. Score 0.364 Round 5: 362 peptides, 54 chains. Longest chain 20 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 308, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gvh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13898 reflections ( 99.67 % complete ) and 15167 restraints for refining 6265 atoms. 13989 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2406 (Rfree = 0.000) for 6265 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2308 (Rfree = 0.000) for 6213 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2329 (Rfree = 0.000) for 6178 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2207 (Rfree = 0.000) for 6148 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:48:56 GMT 2018 Job finished. TimeTaking 86.21 Used memory is bytes: 11307904