null Mon 24 Dec 00:47:36 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gvh-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.6-parrot-mrncs ############### 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 00:47:41 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.6-parrot-mrncs/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-mrncs.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-mrncs.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 7624 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3544 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3273 (Rfree = 0.000) for 7624 atoms. Found 48 (48 requested) and removed 142 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.24 Search for helices and strands: 0 residues in 0 chains, 7614 seeds are put forward NCS extension: 0 residues added, 7614 seeds are put forward Round 1: 384 peptides, 67 chains. Longest chain 12 peptides. Score 0.353 Round 2: 451 peptides, 71 chains. Longest chain 15 peptides. Score 0.422 Round 3: 470 peptides, 60 chains. Longest chain 24 peptides. Score 0.508 Round 4: 475 peptides, 69 chains. Longest chain 19 peptides. Score 0.464 Round 5: 452 peptides, 60 chains. Longest chain 24 peptides. Score 0.486 Taking the results from Round 3 Chains 69, Residues 410, Estimated correctness of the model 0.0 % 11 chains (90 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 13540 restraints for refining 6265 atoms. 11662 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2572 (Rfree = 0.000) for 6265 atoms. Found 28 (40 requested) and removed 50 (20 requested) atoms. Cycle 2: After refmac, R = 0.2384 (Rfree = 0.000) for 6166 atoms. Found 13 (40 requested) and removed 39 (20 requested) atoms. Cycle 3: After refmac, R = 0.2370 (Rfree = 0.000) for 6113 atoms. Found 14 (39 requested) and removed 33 (19 requested) atoms. Cycle 4: After refmac, R = 0.2343 (Rfree = 0.000) for 6073 atoms. Found 16 (39 requested) and removed 24 (19 requested) atoms. Cycle 5: After refmac, R = 0.2302 (Rfree = 0.000) for 6060 atoms. Found 12 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 6227 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 6237 seeds are put forward Round 1: 443 peptides, 67 chains. Longest chain 18 peptides. Score 0.435 Round 2: 484 peptides, 61 chains. Longest chain 25 peptides. Score 0.519 Round 3: 467 peptides, 58 chains. Longest chain 30 peptides. Score 0.515 Round 4: 484 peptides, 58 chains. Longest chain 28 peptides. Score 0.535 Round 5: 499 peptides, 60 chains. Longest chain 21 peptides. Score 0.542 Taking the results from Round 5 Chains 62, Residues 439, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 13991 restraints for refining 6265 atoms. 12164 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2607 (Rfree = 0.000) for 6265 atoms. Found 25 (40 requested) and removed 41 (20 requested) atoms. Cycle 7: After refmac, R = 0.2505 (Rfree = 0.000) for 6216 atoms. Found 27 (40 requested) and removed 66 (20 requested) atoms. Cycle 8: After refmac, R = 0.2810 (Rfree = 0.000) for 6153 atoms. Found 39 (39 requested) and removed 67 (19 requested) atoms. Cycle 9: After refmac, R = 0.2337 (Rfree = 0.000) for 6103 atoms. Found 23 (39 requested) and removed 49 (19 requested) atoms. Cycle 10: After refmac, R = 0.2234 (Rfree = 0.000) for 6054 atoms. Found 20 (38 requested) and removed 34 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.17 Search for helices and strands: 0 residues in 0 chains, 6205 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6226 seeds are put forward Round 1: 437 peptides, 69 chains. Longest chain 19 peptides. Score 0.415 Round 2: 472 peptides, 63 chains. Longest chain 24 peptides. Score 0.494 Round 3: 501 peptides, 57 chains. Longest chain 29 peptides. Score 0.559 Round 4: 507 peptides, 62 chains. Longest chain 32 peptides. Score 0.540 Round 5: 509 peptides, 60 chains. Longest chain 19 peptides. Score 0.553 Taking the results from Round 3 Chains 65, Residues 444, Estimated correctness of the model 0.0 % 8 chains (71 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 13205 restraints for refining 6266 atoms. 11262 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2482 (Rfree = 0.000) for 6266 atoms. Found 36 (40 requested) and removed 45 (20 requested) atoms. Cycle 12: After refmac, R = 0.2705 (Rfree = 0.000) for 6217 atoms. Found 40 (40 requested) and removed 53 (20 requested) atoms. Cycle 13: After refmac, R = 0.2484 (Rfree = 0.000) for 6169 atoms. Found 39 (39 requested) and removed 29 (19 requested) atoms. Cycle 14: After refmac, R = 0.2220 (Rfree = 0.000) for 6166 atoms. Found 26 (39 requested) and removed 31 (19 requested) atoms. Cycle 15: After refmac, R = 0.2653 (Rfree = 0.000) for 6139 atoms. Found 39 (39 requested) and removed 52 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.20 Search for helices and strands: 0 residues in 0 chains, 6267 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6290 seeds are put forward Round 1: 449 peptides, 72 chains. Longest chain 19 peptides. Score 0.413 Round 2: 498 peptides, 67 chains. Longest chain 19 peptides. Score 0.503 Round 3: 480 peptides, 56 chains. Longest chain 30 peptides. Score 0.541 Round 4: 495 peptides, 56 chains. Longest chain 28 peptides. Score 0.558 Round 5: 478 peptides, 58 chains. Longest chain 24 peptides. Score 0.528 Taking the results from Round 4 Chains 62, Residues 439, Estimated correctness of the model 0.0 % 8 chains (69 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 13443 restraints for refining 6265 atoms. 11492 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2380 (Rfree = 0.000) for 6265 atoms. Found 28 (40 requested) and removed 42 (20 requested) atoms. Cycle 17: After refmac, R = 0.2279 (Rfree = 0.000) for 6207 atoms. Found 17 (40 requested) and removed 31 (20 requested) atoms. Cycle 18: After refmac, R = 0.2301 (Rfree = 0.000) for 6176 atoms. Found 25 (39 requested) and removed 47 (19 requested) atoms. Cycle 19: After refmac, R = 0.2204 (Rfree = 0.000) for 6142 atoms. Found 31 (39 requested) and removed 38 (19 requested) atoms. Cycle 20: After refmac, R = 0.2572 (Rfree = 0.000) for 6104 atoms. Found 39 (39 requested) and removed 44 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.17 Search for helices and strands: 0 residues in 0 chains, 6274 seeds are put forward NCS extension: 43 residues added (0 deleted due to clashes), 6317 seeds are put forward Round 1: 416 peptides, 61 chains. Longest chain 21 peptides. Score 0.434 Round 2: 471 peptides, 58 chains. Longest chain 27 peptides. Score 0.520 Round 3: 475 peptides, 57 chains. Longest chain 28 peptides. Score 0.530 Round 4: 462 peptides, 54 chains. Longest chain 19 peptides. Score 0.531 Round 5: 461 peptides, 54 chains. Longest chain 24 peptides. Score 0.530 Taking the results from Round 4 Chains 58, Residues 408, Estimated correctness of the model 0.0 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 13940 restraints for refining 6265 atoms. 12193 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2443 (Rfree = 0.000) for 6265 atoms. Found 36 (40 requested) and removed 36 (20 requested) atoms. Cycle 22: After refmac, R = 0.2313 (Rfree = 0.000) for 6234 atoms. Found 39 (40 requested) and removed 51 (20 requested) atoms. Cycle 23: After refmac, R = 0.2182 (Rfree = 0.000) for 6207 atoms. Found 36 (39 requested) and removed 38 (19 requested) atoms. Cycle 24: After refmac, R = 0.2078 (Rfree = 0.000) for 6195 atoms. Found 30 (39 requested) and removed 39 (19 requested) atoms. Cycle 25: After refmac, R = 0.2021 (Rfree = 0.000) for 6174 atoms. Found 27 (39 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.18 Search for helices and strands: 0 residues in 0 chains, 6302 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6321 seeds are put forward Round 1: 406 peptides, 69 chains. Longest chain 26 peptides. Score 0.372 Round 2: 424 peptides, 58 chains. Longest chain 28 peptides. Score 0.463 Round 3: 462 peptides, 61 chains. Longest chain 50 peptides. Score 0.493 Round 4: 466 peptides, 56 chains. Longest chain 28 peptides. Score 0.525 Round 5: 451 peptides, 57 chains. Longest chain 28 peptides. Score 0.502 Taking the results from Round 4 Chains 60, Residues 410, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14003 restraints for refining 6266 atoms. 12253 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2259 (Rfree = 0.000) for 6266 atoms. Found 32 (40 requested) and removed 30 (20 requested) atoms. Cycle 27: After refmac, R = 0.2216 (Rfree = 0.000) for 6234 atoms. Found 19 (40 requested) and removed 35 (20 requested) atoms. Cycle 28: After refmac, R = 0.2055 (Rfree = 0.000) for 6206 atoms. Found 15 (39 requested) and removed 22 (19 requested) atoms. Cycle 29: After refmac, R = 0.2177 (Rfree = 0.000) for 6183 atoms. Found 27 (39 requested) and removed 36 (19 requested) atoms. Cycle 30: After refmac, R = 0.2588 (Rfree = 0.000) for 6164 atoms. Found 39 (39 requested) and removed 44 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.20 Search for helices and strands: 0 residues in 0 chains, 6334 seeds are put forward NCS extension: 41 residues added (4 deleted due to clashes), 6375 seeds are put forward Round 1: 379 peptides, 65 chains. Longest chain 23 peptides. Score 0.359 Round 2: 423 peptides, 61 chains. Longest chain 17 peptides. Score 0.444 Round 3: 416 peptides, 54 chains. Longest chain 30 peptides. Score 0.476 Round 4: 409 peptides, 52 chains. Longest chain 21 peptides. Score 0.478 Round 5: 429 peptides, 58 chains. Longest chain 23 peptides. Score 0.469 Taking the results from Round 4 Chains 55, Residues 357, Estimated correctness of the model 0.0 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14342 restraints for refining 6266 atoms. 12840 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2304 (Rfree = 0.000) for 6266 atoms. Found 32 (40 requested) and removed 34 (20 requested) atoms. Cycle 32: After refmac, R = 0.2166 (Rfree = 0.000) for 6237 atoms. Found 35 (40 requested) and removed 33 (20 requested) atoms. Cycle 33: After refmac, R = 0.1978 (Rfree = 0.000) for 6224 atoms. Found 20 (40 requested) and removed 29 (20 requested) atoms. Cycle 34: After refmac, R = 0.1970 (Rfree = 0.000) for 6202 atoms. Found 26 (39 requested) and removed 34 (19 requested) atoms. Cycle 35: After refmac, R = 0.2602 (Rfree = 0.000) for 6188 atoms. Found 39 (39 requested) and removed 67 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.21 Search for helices and strands: 0 residues in 0 chains, 6351 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6375 seeds are put forward Round 1: 390 peptides, 69 chains. Longest chain 13 peptides. Score 0.350 Round 2: 379 peptides, 59 chains. Longest chain 16 peptides. Score 0.397 Round 3: 411 peptides, 59 chains. Longest chain 19 peptides. Score 0.440 Round 4: 419 peptides, 59 chains. Longest chain 16 peptides. Score 0.450 Round 5: 436 peptides, 61 chains. Longest chain 17 peptides. Score 0.460 Taking the results from Round 5 Chains 61, Residues 375, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14584 restraints for refining 6266 atoms. 13072 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2162 (Rfree = 0.000) for 6266 atoms. Found 30 (40 requested) and removed 27 (20 requested) atoms. Cycle 37: After refmac, R = 0.1920 (Rfree = 0.000) for 6250 atoms. Found 15 (40 requested) and removed 22 (20 requested) atoms. Cycle 38: After refmac, R = 0.1862 (Rfree = 0.000) for 6236 atoms. Found 15 (40 requested) and removed 22 (20 requested) atoms. Cycle 39: After refmac, R = 0.1870 (Rfree = 0.000) for 6226 atoms. Found 12 (39 requested) and removed 22 (19 requested) atoms. Cycle 40: After refmac, R = 0.2446 (Rfree = 0.000) for 6214 atoms. Found 39 (39 requested) and removed 32 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.21 Search for helices and strands: 0 residues in 0 chains, 6392 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6409 seeds are put forward Round 1: 348 peptides, 65 chains. Longest chain 11 peptides. Score 0.313 Round 2: 386 peptides, 60 chains. Longest chain 16 peptides. Score 0.400 Round 3: 397 peptides, 58 chains. Longest chain 17 peptides. Score 0.427 Round 4: 412 peptides, 58 chains. Longest chain 16 peptides. Score 0.447 Round 5: 393 peptides, 54 chains. Longest chain 17 peptides. Score 0.446 Taking the results from Round 4 Chains 61, Residues 354, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 13898 reflections ( 99.67 % complete ) and 14165 restraints for refining 6265 atoms. 12694 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2227 (Rfree = 0.000) for 6265 atoms. Found 35 (40 requested) and removed 31 (20 requested) atoms. Cycle 42: After refmac, R = 0.2051 (Rfree = 0.000) for 6238 atoms. Found 18 (40 requested) and removed 24 (20 requested) atoms. Cycle 43: After refmac, R = 0.2041 (Rfree = 0.000) for 6223 atoms. Found 9 (39 requested) and removed 26 (19 requested) atoms. Cycle 44: After refmac, R = 0.1971 (Rfree = 0.000) for 6199 atoms. Found 11 (39 requested) and removed 20 (19 requested) atoms. Cycle 45: After refmac, R = 0.1957 (Rfree = 0.000) for 6187 atoms. Found 12 (39 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.21 Search for helices and strands: 0 residues in 0 chains, 6322 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6335 seeds are put forward Round 1: 387 peptides, 72 chains. Longest chain 15 peptides. Score 0.326 Round 2: 402 peptides, 63 chains. Longest chain 16 peptides. Score 0.404 Round 3: 405 peptides, 60 chains. Longest chain 16 peptides. Score 0.426 Round 4: 403 peptides, 57 chains. Longest chain 16 peptides. Score 0.441 Round 5: 408 peptides, 57 chains. Longest chain 16 peptides. Score 0.448 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 351, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2gvh-3_warpNtrace.pdb as input Building loops using Loopy2018 58 chains (351 residues) following loop building 6 chains (45 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13898 reflections ( 99.67 % complete ) and 14161 restraints for refining 6266 atoms. 12671 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2364 (Rfree = 0.000) for 6266 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2101 (Rfree = 0.000) for 6212 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2015 (Rfree = 0.000) for 6176 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1948 (Rfree = 0.000) for 6151 atoms. Found 0 (39 requested) and removed 12 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:53:53 GMT 2018 Job finished. TimeTaking 66.28 Used memory is bytes: 20905728