Sun 23 Dec 23:44:00 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 2otm-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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/2otm-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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 ============================================================ Sun 23 Dec 23:44:05 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/2otm-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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 378 and 0 Target number of residues in the AU: 378 Target solvent content: 0.6303 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3696 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: 78.536 3.600 Wilson plot Bfac: 66.47 6456 reflections ( 99.77 % complete ) and 0 restraints for refining 4077 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3050 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2868 (Rfree = 0.000) for 4077 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 4148 seeds are put forward NCS extension: 0 residues added, 4148 seeds are put forward Round 1: 237 peptides, 44 chains. Longest chain 13 peptides. Score 0.365 Round 2: 279 peptides, 35 chains. Longest chain 26 peptides. Score 0.578 Round 3: 292 peptides, 37 chains. Longest chain 25 peptides. Score 0.587 Round 4: 285 peptides, 32 chains. Longest chain 20 peptides. Score 0.621 Round 5: 303 peptides, 36 chains. Longest chain 22 peptides. Score 0.620 Taking the results from Round 4 Chains 34, Residues 253, Estimated correctness of the model 22.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7406 restraints for refining 3350 atoms. 6395 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2424 (Rfree = 0.000) for 3350 atoms. Found 12 (21 requested) and removed 27 (10 requested) atoms. Cycle 2: After refmac, R = 0.2257 (Rfree = 0.000) for 3292 atoms. Found 6 (21 requested) and removed 24 (10 requested) atoms. Cycle 3: After refmac, R = 0.2022 (Rfree = 0.000) for 3252 atoms. Found 7 (21 requested) and removed 16 (10 requested) atoms. Cycle 4: After refmac, R = 0.1961 (Rfree = 0.000) for 3232 atoms. Found 2 (20 requested) and removed 18 (10 requested) atoms. Cycle 5: After refmac, R = 0.2021 (Rfree = 0.000) for 3210 atoms. Found 4 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 3329 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 3340 seeds are put forward Round 1: 275 peptides, 43 chains. Longest chain 18 peptides. Score 0.482 Round 2: 294 peptides, 36 chains. Longest chain 22 peptides. Score 0.601 Round 3: 312 peptides, 34 chains. Longest chain 24 peptides. Score 0.657 Round 4: 308 peptides, 38 chains. Longest chain 17 peptides. Score 0.612 Round 5: 294 peptides, 34 chains. Longest chain 17 peptides. Score 0.621 Taking the results from Round 3 Chains 40, Residues 278, Estimated correctness of the model 35.6 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 6840 restraints for refining 3350 atoms. 5614 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2235 (Rfree = 0.000) for 3350 atoms. Found 9 (21 requested) and removed 24 (10 requested) atoms. Cycle 7: After refmac, R = 0.2103 (Rfree = 0.000) for 3318 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2038 (Rfree = 0.000) for 3306 atoms. Found 7 (21 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.1992 (Rfree = 0.000) for 3296 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 10: After refmac, R = 0.1974 (Rfree = 0.000) for 3286 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.11 Search for helices and strands: 0 residues in 0 chains, 3368 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3386 seeds are put forward Round 1: 268 peptides, 38 chains. Longest chain 20 peptides. Score 0.520 Round 2: 285 peptides, 32 chains. Longest chain 27 peptides. Score 0.621 Round 3: 296 peptides, 39 chains. Longest chain 19 peptides. Score 0.576 Round 4: 289 peptides, 35 chains. Longest chain 21 peptides. Score 0.600 Round 5: 285 peptides, 32 chains. Longest chain 22 peptides. Score 0.621 Taking the results from Round 5 Chains 32, Residues 253, Estimated correctness of the model 22.7 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7244 restraints for refining 3350 atoms. 6207 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2152 (Rfree = 0.000) for 3350 atoms. Found 7 (21 requested) and removed 18 (10 requested) atoms. Cycle 12: After refmac, R = 0.2048 (Rfree = 0.000) for 3327 atoms. Found 7 (21 requested) and removed 14 (10 requested) atoms. Cycle 13: After refmac, R = 0.1979 (Rfree = 0.000) for 3310 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1942 (Rfree = 0.000) for 3298 atoms. Found 0 (21 requested) and removed 11 (10 requested) atoms. Cycle 15: After refmac, R = 0.1878 (Rfree = 0.000) for 3283 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 3368 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3389 seeds are put forward Round 1: 265 peptides, 38 chains. Longest chain 32 peptides. Score 0.513 Round 2: 300 peptides, 37 chains. Longest chain 23 peptides. Score 0.604 Round 3: 300 peptides, 36 chains. Longest chain 24 peptides. Score 0.614 Round 4: 307 peptides, 33 chains. Longest chain 26 peptides. Score 0.656 Round 5: 306 peptides, 35 chains. Longest chain 25 peptides. Score 0.636 Taking the results from Round 4 Chains 33, Residues 274, Estimated correctness of the model 35.2 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7133 restraints for refining 3350 atoms. 6052 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2055 (Rfree = 0.000) for 3350 atoms. Found 10 (21 requested) and removed 14 (10 requested) atoms. Cycle 17: After refmac, R = 0.1901 (Rfree = 0.000) for 3336 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. Cycle 18: After refmac, R = 0.1820 (Rfree = 0.000) for 3320 atoms. Found 7 (21 requested) and removed 17 (10 requested) atoms. Cycle 19: After refmac, R = 0.1781 (Rfree = 0.000) for 3308 atoms. Found 4 (21 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.1743 (Rfree = 0.000) for 3298 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 3396 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 3431 seeds are put forward Round 1: 258 peptides, 40 chains. Longest chain 16 peptides. Score 0.472 Round 2: 275 peptides, 32 chains. Longest chain 25 peptides. Score 0.600 Round 3: 268 peptides, 35 chains. Longest chain 19 peptides. Score 0.553 Round 4: 272 peptides, 32 chains. Longest chain 18 peptides. Score 0.593 Round 5: 282 peptides, 32 chains. Longest chain 23 peptides. Score 0.615 Taking the results from Round 5 Chains 32, Residues 250, Estimated correctness of the model 20.4 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7401 restraints for refining 3348 atoms. 6427 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2050 (Rfree = 0.000) for 3348 atoms. Found 16 (21 requested) and removed 18 (10 requested) atoms. Cycle 22: After refmac, R = 0.1860 (Rfree = 0.000) for 3338 atoms. Found 9 (21 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.1816 (Rfree = 0.000) for 3334 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.1780 (Rfree = 0.000) for 3328 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.1763 (Rfree = 0.000) for 3317 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 3402 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 3411 seeds are put forward Round 1: 236 peptides, 39 chains. Longest chain 11 peptides. Score 0.424 Round 2: 275 peptides, 35 chains. Longest chain 21 peptides. Score 0.569 Round 3: 271 peptides, 32 chains. Longest chain 19 peptides. Score 0.591 Round 4: 278 peptides, 36 chains. Longest chain 22 peptides. Score 0.566 Round 5: 276 peptides, 30 chains. Longest chain 23 peptides. Score 0.622 Taking the results from Round 5 Chains 30, Residues 246, Estimated correctness of the model 23.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7449 restraints for refining 3350 atoms. 6495 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2005 (Rfree = 0.000) for 3350 atoms. Found 12 (21 requested) and removed 17 (10 requested) atoms. Cycle 27: After refmac, R = 0.1870 (Rfree = 0.000) for 3330 atoms. Found 4 (21 requested) and removed 12 (10 requested) atoms. Cycle 28: After refmac, R = 0.1911 (Rfree = 0.000) for 3317 atoms. Found 2 (21 requested) and removed 14 (10 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1827 (Rfree = 0.000) for 3302 atoms. Found 6 (21 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1836 (Rfree = 0.000) for 3293 atoms. Found 6 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 3378 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3395 seeds are put forward Round 1: 226 peptides, 36 chains. Longest chain 15 peptides. Score 0.433 Round 2: 247 peptides, 36 chains. Longest chain 16 peptides. Score 0.489 Round 3: 251 peptides, 35 chains. Longest chain 23 peptides. Score 0.511 Round 4: 260 peptides, 34 chains. Longest chain 24 peptides. Score 0.545 Round 5: 260 peptides, 31 chains. Longest chain 30 peptides. Score 0.576 Taking the results from Round 5 Chains 31, Residues 229, Estimated correctness of the model 5.1 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7437 restraints for refining 3349 atoms. 6530 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2128 (Rfree = 0.000) for 3349 atoms. Found 12 (21 requested) and removed 26 (10 requested) atoms. Cycle 32: After refmac, R = 0.1986 (Rfree = 0.000) for 3331 atoms. Found 3 (21 requested) and removed 16 (10 requested) atoms. Cycle 33: After refmac, R = 0.1932 (Rfree = 0.000) for 3314 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. Cycle 34: After refmac, R = 0.1953 (Rfree = 0.000) for 3303 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. Cycle 35: After refmac, R = 0.1871 (Rfree = 0.000) for 3289 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.11 Search for helices and strands: 0 residues in 0 chains, 3379 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 3414 seeds are put forward Round 1: 207 peptides, 34 chains. Longest chain 12 peptides. Score 0.403 Round 2: 242 peptides, 34 chains. Longest chain 16 peptides. Score 0.500 Round 3: 242 peptides, 33 chains. Longest chain 24 peptides. Score 0.511 Round 4: 234 peptides, 29 chains. Longest chain 21 peptides. Score 0.537 Round 5: 226 peptides, 31 chains. Longest chain 21 peptides. Score 0.493 Taking the results from Round 4 Chains 30, Residues 205, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7513 restraints for refining 3350 atoms. 6650 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2120 (Rfree = 0.000) for 3350 atoms. Found 11 (21 requested) and removed 20 (10 requested) atoms. Cycle 37: After refmac, R = 0.1955 (Rfree = 0.000) for 3331 atoms. Found 6 (21 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.1918 (Rfree = 0.000) for 3316 atoms. Found 10 (21 requested) and removed 14 (10 requested) atoms. Cycle 39: After refmac, R = 0.1776 (Rfree = 0.000) for 3309 atoms. Found 4 (21 requested) and removed 15 (10 requested) atoms. Cycle 40: After refmac, R = 0.1706 (Rfree = 0.000) for 3293 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 3368 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3392 seeds are put forward Round 1: 190 peptides, 30 chains. Longest chain 11 peptides. Score 0.405 Round 2: 225 peptides, 32 chains. Longest chain 17 peptides. Score 0.478 Round 3: 230 peptides, 32 chains. Longest chain 14 peptides. Score 0.492 Round 4: 240 peptides, 34 chains. Longest chain 21 peptides. Score 0.494 Round 5: 227 peptides, 30 chains. Longest chain 19 peptides. Score 0.507 Taking the results from Round 5 Chains 30, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7649 restraints for refining 3350 atoms. 6891 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1979 (Rfree = 0.000) for 3350 atoms. Found 10 (21 requested) and removed 14 (10 requested) atoms. Cycle 42: After refmac, R = 0.1900 (Rfree = 0.000) for 3337 atoms. Found 2 (21 requested) and removed 15 (10 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1704 (Rfree = 0.000) for 3319 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.1679 (Rfree = 0.000) for 3308 atoms. Found 2 (21 requested) and removed 14 (10 requested) atoms. Cycle 45: After refmac, R = 0.1645 (Rfree = 0.000) for 3292 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 3362 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 3394 seeds are put forward Round 1: 224 peptides, 37 chains. Longest chain 12 peptides. Score 0.414 Round 2: 236 peptides, 38 chains. Longest chain 18 peptides. Score 0.436 Round 3: 230 peptides, 32 chains. Longest chain 15 peptides. Score 0.492 Round 4: 227 peptides, 30 chains. Longest chain 28 peptides. Score 0.507 Round 5: 244 peptides, 34 chains. Longest chain 15 peptides. Score 0.505 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 197, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (197 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6456 reflections ( 99.77 % complete ) and 7435 restraints for refining 3350 atoms. 6598 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2078 (Rfree = 0.000) for 3350 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1903 (Rfree = 0.000) for 3328 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1843 (Rfree = 0.000) for 3313 atoms. Found 0 (21 requested) and removed 9 (10 requested) atoms. Cycle 49: After refmac, R = 0.1797 (Rfree = 0.000) for 3303 atoms. TimeTaking 44.92