Mon 24 Dec 07:59:42 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 1vpm-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vpm-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vpm-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.8-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/1vpm-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.8-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 07:59:47 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/1vpm-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.8-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 329 and 0 Target number of residues in the AU: 329 Target solvent content: 0.6645 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 507 Adjusted target solvent content: 0.48 Input MTZ file: 1vpm-3.8-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 4056 target number of atoms Had to go as low as 0.60 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: 79.699 3.801 Wilson plot Bfac: 87.91 5369 reflections ( 97.71 % complete ) and 0 restraints for refining 4471 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3260 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2549 (Rfree = 0.000) for 4471 atoms. Found 9 (24 requested) and removed 63 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 4473 seeds are put forward NCS extension: 0 residues added, 4473 seeds are put forward Round 1: 211 peptides, 43 chains. Longest chain 11 peptides. Score 0.302 Round 2: 274 peptides, 41 chains. Longest chain 19 peptides. Score 0.512 Round 3: 281 peptides, 34 chains. Longest chain 19 peptides. Score 0.605 Round 4: 294 peptides, 41 chains. Longest chain 19 peptides. Score 0.562 Round 5: 290 peptides, 37 chains. Longest chain 19 peptides. Score 0.594 Taking the results from Round 3 Chains 37, Residues 247, Estimated correctness of the model 1.1 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8250 restraints for refining 3668 atoms. 7210 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2455 (Rfree = 0.000) for 3668 atoms. Found 6 (20 requested) and removed 32 (10 requested) atoms. Cycle 2: After refmac, R = 0.2368 (Rfree = 0.000) for 3552 atoms. Found 14 (20 requested) and removed 21 (10 requested) atoms. Cycle 3: After refmac, R = 0.2143 (Rfree = 0.000) for 3504 atoms. Found 10 (19 requested) and removed 41 (9 requested) atoms. Cycle 4: After refmac, R = 0.2038 (Rfree = 0.000) for 3444 atoms. Found 10 (19 requested) and removed 31 (9 requested) atoms. Cycle 5: After refmac, R = 0.2014 (Rfree = 0.000) for 3404 atoms. Found 17 (18 requested) and removed 34 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 3532 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3549 seeds are put forward Round 1: 240 peptides, 41 chains. Longest chain 11 peptides. Score 0.418 Round 2: 263 peptides, 38 chains. Longest chain 16 peptides. Score 0.518 Round 3: 280 peptides, 39 chains. Longest chain 23 peptides. Score 0.550 Round 4: 284 peptides, 35 chains. Longest chain 16 peptides. Score 0.601 Round 5: 282 peptides, 36 chains. Longest chain 39 peptides. Score 0.586 Taking the results from Round 4 Chains 39, Residues 249, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7546 restraints for refining 3475 atoms. 6480 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2209 (Rfree = 0.000) for 3475 atoms. Found 18 (19 requested) and removed 48 (9 requested) atoms. Cycle 7: After refmac, R = 0.1891 (Rfree = 0.000) for 3421 atoms. Found 5 (18 requested) and removed 25 (9 requested) atoms. Cycle 8: After refmac, R = 0.1827 (Rfree = 0.000) for 3386 atoms. Found 7 (18 requested) and removed 19 (9 requested) atoms. Cycle 9: After refmac, R = 0.1766 (Rfree = 0.000) for 3367 atoms. Found 5 (18 requested) and removed 22 (9 requested) atoms. Cycle 10: After refmac, R = 0.1719 (Rfree = 0.000) for 3340 atoms. Found 9 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 3428 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3447 seeds are put forward Round 1: 257 peptides, 43 chains. Longest chain 14 peptides. Score 0.443 Round 2: 278 peptides, 39 chains. Longest chain 20 peptides. Score 0.545 Round 3: 284 peptides, 37 chains. Longest chain 21 peptides. Score 0.580 Round 4: 294 peptides, 37 chains. Longest chain 19 peptides. Score 0.603 Round 5: 285 peptides, 38 chains. Longest chain 17 peptides. Score 0.572 Taking the results from Round 4 Chains 40, Residues 257, Estimated correctness of the model 0.2 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7703 restraints for refining 3525 atoms. 6613 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2198 (Rfree = 0.000) for 3525 atoms. Found 17 (19 requested) and removed 31 (9 requested) atoms. Cycle 12: After refmac, R = 0.1956 (Rfree = 0.000) for 3471 atoms. Found 7 (19 requested) and removed 24 (9 requested) atoms. Cycle 13: After refmac, R = 0.1928 (Rfree = 0.000) for 3432 atoms. Found 9 (18 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.1833 (Rfree = 0.000) for 3411 atoms. Found 10 (18 requested) and removed 14 (9 requested) atoms. Cycle 15: After refmac, R = 0.1805 (Rfree = 0.000) for 3396 atoms. Found 11 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 3478 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 3496 seeds are put forward Round 1: 236 peptides, 37 chains. Longest chain 15 peptides. Score 0.457 Round 2: 262 peptides, 35 chains. Longest chain 20 peptides. Score 0.549 Round 3: 264 peptides, 36 chains. Longest chain 18 peptides. Score 0.543 Round 4: 266 peptides, 32 chains. Longest chain 23 peptides. Score 0.591 Round 5: 260 peptides, 35 chains. Longest chain 22 peptides. Score 0.544 Taking the results from Round 4 Chains 32, Residues 234, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7922 restraints for refining 3541 atoms. 6968 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2109 (Rfree = 0.000) for 3541 atoms. Found 19 (19 requested) and removed 111 (9 requested) atoms. Cycle 17: After refmac, R = 0.2032 (Rfree = 0.000) for 3431 atoms. Found 18 (18 requested) and removed 39 (9 requested) atoms. Cycle 18: After refmac, R = 0.1866 (Rfree = 0.000) for 3382 atoms. Found 9 (18 requested) and removed 26 (9 requested) atoms. Cycle 19: After refmac, R = 0.1851 (Rfree = 0.000) for 3337 atoms. Found 11 (18 requested) and removed 15 (9 requested) atoms. Cycle 20: After refmac, R = 0.1818 (Rfree = 0.000) for 3313 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 3443 seeds are put forward NCS extension: 25 residues added (11 deleted due to clashes), 3468 seeds are put forward Round 1: 180 peptides, 34 chains. Longest chain 10 peptides. Score 0.325 Round 2: 237 peptides, 37 chains. Longest chain 16 peptides. Score 0.460 Round 3: 250 peptides, 34 chains. Longest chain 16 peptides. Score 0.530 Round 4: 243 peptides, 33 chains. Longest chain 19 peptides. Score 0.524 Round 5: 254 peptides, 32 chains. Longest chain 21 peptides. Score 0.563 Taking the results from Round 5 Chains 33, Residues 222, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7600 restraints for refining 3363 atoms. 6718 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2197 (Rfree = 0.000) for 3363 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 22: After refmac, R = 0.2058 (Rfree = 0.000) for 3331 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.1987 (Rfree = 0.000) for 3311 atoms. Found 16 (18 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.1646 (Rfree = 0.000) for 3293 atoms. Found 5 (18 requested) and removed 14 (9 requested) atoms. Cycle 25: After refmac, R = 0.1503 (Rfree = 0.000) for 3274 atoms. Found 6 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 3394 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3419 seeds are put forward Round 1: 158 peptides, 28 chains. Longest chain 14 peptides. Score 0.338 Round 2: 222 peptides, 32 chains. Longest chain 19 peptides. Score 0.479 Round 3: 235 peptides, 36 chains. Longest chain 19 peptides. Score 0.466 Round 4: 246 peptides, 32 chains. Longest chain 20 peptides. Score 0.543 Round 5: 233 peptides, 38 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 4 Chains 32, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7550 restraints for refining 3327 atoms. 6726 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2041 (Rfree = 0.000) for 3327 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 27: After refmac, R = 0.2055 (Rfree = 0.000) for 3297 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 28: After refmac, R = 0.2025 (Rfree = 0.000) for 3284 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.1846 (Rfree = 0.000) for 3276 atoms. Found 17 (18 requested) and removed 15 (9 requested) atoms. Cycle 30: After refmac, R = 0.1869 (Rfree = 0.000) for 3276 atoms. Found 13 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 3403 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 3427 seeds are put forward Round 1: 195 peptides, 36 chains. Longest chain 13 peptides. Score 0.346 Round 2: 216 peptides, 33 chains. Longest chain 13 peptides. Score 0.450 Round 3: 235 peptides, 32 chains. Longest chain 18 peptides. Score 0.515 Round 4: 242 peptides, 33 chains. Longest chain 19 peptides. Score 0.521 Round 5: 236 peptides, 30 chains. Longest chain 18 peptides. Score 0.541 Taking the results from Round 5 Chains 30, Residues 206, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7942 restraints for refining 3483 atoms. 7148 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2294 (Rfree = 0.000) for 3483 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 32: After refmac, R = 0.2077 (Rfree = 0.000) for 3456 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 33: After refmac, R = 0.2128 (Rfree = 0.000) for 3440 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 34: After refmac, R = 0.1912 (Rfree = 0.000) for 3423 atoms. Found 15 (18 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1909 (Rfree = 0.000) for 3416 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 3518 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3534 seeds are put forward Round 1: 177 peptides, 33 chains. Longest chain 14 peptides. Score 0.329 Round 2: 203 peptides, 34 chains. Longest chain 13 peptides. Score 0.398 Round 3: 216 peptides, 35 chains. Longest chain 13 peptides. Score 0.424 Round 4: 216 peptides, 32 chains. Longest chain 16 peptides. Score 0.462 Round 5: 217 peptides, 33 chains. Longest chain 16 peptides. Score 0.453 Taking the results from Round 4 Chains 32, Residues 184, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7952 restraints for refining 3465 atoms. 7187 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2130 (Rfree = 0.000) for 3465 atoms. Found 19 (19 requested) and removed 80 (9 requested) atoms. Cycle 37: After refmac, R = 0.1945 (Rfree = 0.000) for 3392 atoms. Found 13 (18 requested) and removed 33 (9 requested) atoms. Cycle 38: After refmac, R = 0.1799 (Rfree = 0.000) for 3363 atoms. Found 8 (18 requested) and removed 24 (9 requested) atoms. Cycle 39: After refmac, R = 0.1767 (Rfree = 0.000) for 3343 atoms. Found 11 (18 requested) and removed 19 (9 requested) atoms. Cycle 40: After refmac, R = 0.1637 (Rfree = 0.000) for 3329 atoms. Found 8 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 3437 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3457 seeds are put forward Round 1: 183 peptides, 39 chains. Longest chain 9 peptides. Score 0.264 Round 2: 198 peptides, 32 chains. Longest chain 14 peptides. Score 0.410 Round 3: 186 peptides, 29 chains. Longest chain 13 peptides. Score 0.413 Round 4: 194 peptides, 31 chains. Longest chain 16 peptides. Score 0.411 Round 5: 205 peptides, 32 chains. Longest chain 14 peptides. Score 0.431 Taking the results from Round 5 Chains 34, Residues 173, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7662 restraints for refining 3439 atoms. 6940 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1913 (Rfree = 0.000) for 3439 atoms. Found 17 (18 requested) and removed 46 (9 requested) atoms. Cycle 42: After refmac, R = 0.1901 (Rfree = 0.000) for 3394 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 43: After refmac, R = 0.1823 (Rfree = 0.000) for 3375 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.1807 (Rfree = 0.000) for 3367 atoms. Found 13 (18 requested) and removed 19 (9 requested) atoms. Cycle 45: After refmac, R = 0.1804 (Rfree = 0.000) for 3342 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 3446 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3464 seeds are put forward Round 1: 150 peptides, 34 chains. Longest chain 8 peptides. Score 0.220 Round 2: 175 peptides, 31 chains. Longest chain 15 peptides. Score 0.351 Round 3: 187 peptides, 33 chains. Longest chain 15 peptides. Score 0.362 Round 4: 193 peptides, 31 chains. Longest chain 12 peptides. Score 0.408 Round 5: 187 peptides, 31 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 162, 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 1vpm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5369 reflections ( 97.71 % complete ) and 7750 restraints for refining 3365 atoms. 7133 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2099 (Rfree = 0.000) for 3365 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2161 (Rfree = 0.000) for 3338 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2026 (Rfree = 0.000) for 3315 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2163 (Rfree = 0.000) for 3299 atoms. TimeTaking 40.52