Mon 24 Dec 00:14:38 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 2op5-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-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/2op5-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-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 00:14:43 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/2op5-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-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 458 and 0 Target number of residues in the AU: 458 Target solvent content: 0.6428 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-4.0-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: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 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: 73.087 4.000 Wilson plot Bfac: 73.49 6261 reflections ( 99.73 % complete ) and 0 restraints for refining 6203 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3358 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3331 (Rfree = 0.000) for 6203 atoms. Found 21 (29 requested) and removed 48 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.88 Search for helices and strands: 0 residues in 0 chains, 6326 seeds are put forward NCS extension: 0 residues added, 6326 seeds are put forward Round 1: 214 peptides, 45 chains. Longest chain 7 peptides. Score 0.263 Round 2: 289 peptides, 52 chains. Longest chain 12 peptides. Score 0.377 Round 3: 305 peptides, 51 chains. Longest chain 11 peptides. Score 0.424 Round 4: 310 peptides, 51 chains. Longest chain 13 peptides. Score 0.435 Round 5: 329 peptides, 52 chains. Longest chain 11 peptides. Score 0.467 Taking the results from Round 5 Chains 52, Residues 277, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 12010 restraints for refining 5039 atoms. 10954 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2985 (Rfree = 0.000) for 5039 atoms. Found 13 (23 requested) and removed 59 (11 requested) atoms. Cycle 2: After refmac, R = 0.2875 (Rfree = 0.000) for 4884 atoms. Found 12 (23 requested) and removed 54 (11 requested) atoms. Cycle 3: After refmac, R = 0.2546 (Rfree = 0.000) for 4775 atoms. Found 8 (23 requested) and removed 42 (11 requested) atoms. Cycle 4: After refmac, R = 0.2680 (Rfree = 0.000) for 4696 atoms. Found 8 (22 requested) and removed 43 (11 requested) atoms. Cycle 5: After refmac, R = 0.2842 (Rfree = 0.000) for 4622 atoms. Found 18 (22 requested) and removed 38 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 4805 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4817 seeds are put forward Round 1: 272 peptides, 60 chains. Longest chain 8 peptides. Score 0.252 Round 2: 294 peptides, 55 chains. Longest chain 10 peptides. Score 0.359 Round 3: 306 peptides, 52 chains. Longest chain 17 peptides. Score 0.417 Round 4: 301 peptides, 52 chains. Longest chain 14 peptides. Score 0.405 Round 5: 311 peptides, 51 chains. Longest chain 14 peptides. Score 0.437 Taking the results from Round 5 Chains 51, Residues 260, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11479 restraints for refining 4857 atoms. 10490 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2638 (Rfree = 0.000) for 4857 atoms. Found 6 (23 requested) and removed 73 (11 requested) atoms. Cycle 7: After refmac, R = 0.2546 (Rfree = 0.000) for 4736 atoms. Found 8 (22 requested) and removed 38 (11 requested) atoms. Cycle 8: After refmac, R = 0.2446 (Rfree = 0.000) for 4667 atoms. Found 3 (22 requested) and removed 50 (11 requested) atoms. Cycle 9: After refmac, R = 0.2487 (Rfree = 0.000) for 4590 atoms. Found 9 (21 requested) and removed 37 (10 requested) atoms. Cycle 10: After refmac, R = 0.2405 (Rfree = 0.000) for 4540 atoms. Found 6 (21 requested) and removed 29 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.80 Search for helices and strands: 0 residues in 0 chains, 4710 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4727 seeds are put forward Round 1: 251 peptides, 47 chains. Longest chain 11 peptides. Score 0.337 Round 2: 264 peptides, 44 chains. Longest chain 13 peptides. Score 0.400 Round 3: 298 peptides, 47 chains. Longest chain 17 peptides. Score 0.447 Round 4: 312 peptides, 51 chains. Longest chain 18 peptides. Score 0.440 Round 5: 305 peptides, 49 chains. Longest chain 17 peptides. Score 0.443 Taking the results from Round 3 Chains 47, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 10485 restraints for refining 4637 atoms. 9528 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2672 (Rfree = 0.000) for 4637 atoms. Found 17 (22 requested) and removed 45 (11 requested) atoms. Cycle 12: After refmac, R = 0.2625 (Rfree = 0.000) for 4578 atoms. Found 14 (21 requested) and removed 40 (10 requested) atoms. Cycle 13: After refmac, R = 0.2477 (Rfree = 0.000) for 4521 atoms. Found 13 (21 requested) and removed 30 (10 requested) atoms. Cycle 14: After refmac, R = 0.1998 (Rfree = 0.000) for 4480 atoms. Found 6 (21 requested) and removed 15 (10 requested) atoms. Cycle 15: After refmac, R = 0.2034 (Rfree = 0.000) for 4454 atoms. Found 2 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 4600 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 4627 seeds are put forward Round 1: 228 peptides, 45 chains. Longest chain 9 peptides. Score 0.300 Round 2: 295 peptides, 53 chains. Longest chain 11 peptides. Score 0.381 Round 3: 296 peptides, 49 chains. Longest chain 12 peptides. Score 0.423 Round 4: 301 peptides, 50 chains. Longest chain 12 peptides. Score 0.425 Round 5: 311 peptides, 54 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 4 Chains 50, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 10166 restraints for refining 4545 atoms. 9212 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2675 (Rfree = 0.000) for 4545 atoms. Found 17 (21 requested) and removed 46 (10 requested) atoms. Cycle 17: After refmac, R = 0.2512 (Rfree = 0.000) for 4492 atoms. Found 12 (21 requested) and removed 22 (10 requested) atoms. Cycle 18: After refmac, R = 0.2462 (Rfree = 0.000) for 4459 atoms. Found 11 (21 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.2391 (Rfree = 0.000) for 4432 atoms. Found 6 (21 requested) and removed 26 (10 requested) atoms. Cycle 20: After refmac, R = 0.2224 (Rfree = 0.000) for 4386 atoms. Found 11 (20 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 4515 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4530 seeds are put forward Round 1: 218 peptides, 46 chains. Longest chain 10 peptides. Score 0.263 Round 2: 257 peptides, 44 chains. Longest chain 11 peptides. Score 0.383 Round 3: 272 peptides, 47 chains. Longest chain 13 peptides. Score 0.388 Round 4: 270 peptides, 42 chains. Longest chain 15 peptides. Score 0.434 Round 5: 284 peptides, 46 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 4 Chains 42, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 9991 restraints for refining 4464 atoms. 9121 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2256 (Rfree = 0.000) for 4464 atoms. Found 9 (21 requested) and removed 30 (10 requested) atoms. Cycle 22: After refmac, R = 0.2344 (Rfree = 0.000) for 4413 atoms. Found 11 (21 requested) and removed 27 (10 requested) atoms. Cycle 23: After refmac, R = 0.1911 (Rfree = 0.000) for 4368 atoms. Found 2 (20 requested) and removed 17 (10 requested) atoms. Cycle 24: After refmac, R = 0.1802 (Rfree = 0.000) for 4333 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.1704 (Rfree = 0.000) for 4323 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.83 Search for helices and strands: 0 residues in 0 chains, 4434 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4452 seeds are put forward Round 1: 233 peptides, 48 chains. Longest chain 9 peptides. Score 0.280 Round 2: 264 peptides, 47 chains. Longest chain 13 peptides. Score 0.369 Round 3: 261 peptides, 47 chains. Longest chain 12 peptides. Score 0.362 Round 4: 241 peptides, 39 chains. Longest chain 12 peptides. Score 0.397 Round 5: 249 peptides, 40 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 5 Chains 40, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 10822 restraints for refining 4631 atoms. 10026 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2225 (Rfree = 0.000) for 4631 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 27: After refmac, R = 0.1822 (Rfree = 0.000) for 4594 atoms. Found 9 (21 requested) and removed 16 (10 requested) atoms. Cycle 28: After refmac, R = 0.1752 (Rfree = 0.000) for 4578 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.1783 (Rfree = 0.000) for 4565 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1736 (Rfree = 0.000) for 4559 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 4662 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4677 seeds are put forward Round 1: 208 peptides, 44 chains. Longest chain 10 peptides. Score 0.258 Round 2: 254 peptides, 48 chains. Longest chain 13 peptides. Score 0.334 Round 3: 267 peptides, 48 chains. Longest chain 10 peptides. Score 0.366 Round 4: 263 peptides, 45 chains. Longest chain 11 peptides. Score 0.387 Round 5: 252 peptides, 43 chains. Longest chain 10 peptides. Score 0.382 Taking the results from Round 4 Chains 45, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 10918 restraints for refining 4732 atoms. 10091 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2144 (Rfree = 0.000) for 4732 atoms. Found 11 (22 requested) and removed 38 (11 requested) atoms. Cycle 32: After refmac, R = 0.1891 (Rfree = 0.000) for 4675 atoms. Found 4 (22 requested) and removed 24 (11 requested) atoms. Cycle 33: After refmac, R = 0.1910 (Rfree = 0.000) for 4632 atoms. Found 6 (22 requested) and removed 21 (11 requested) atoms. Cycle 34: After refmac, R = 0.1946 (Rfree = 0.000) for 4602 atoms. Found 8 (21 requested) and removed 17 (10 requested) atoms. Cycle 35: After refmac, R = 0.1556 (Rfree = 0.000) for 4569 atoms. Found 1 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.81 Search for helices and strands: 0 residues in 0 chains, 4646 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4661 seeds are put forward Round 1: 196 peptides, 44 chains. Longest chain 7 peptides. Score 0.225 Round 2: 218 peptides, 44 chains. Longest chain 7 peptides. Score 0.285 Round 3: 221 peptides, 39 chains. Longest chain 14 peptides. Score 0.348 Round 4: 240 peptides, 42 chains. Longest chain 11 peptides. Score 0.363 Round 5: 228 peptides, 43 chains. Longest chain 9 peptides. Score 0.322 Taking the results from Round 4 Chains 42, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 10560 restraints for refining 4552 atoms. 9810 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1976 (Rfree = 0.000) for 4552 atoms. Found 11 (21 requested) and removed 35 (10 requested) atoms. Cycle 37: After refmac, R = 0.1878 (Rfree = 0.000) for 4510 atoms. Found 10 (21 requested) and removed 18 (10 requested) atoms. Cycle 38: After refmac, R = 0.1856 (Rfree = 0.000) for 4489 atoms. Found 15 (21 requested) and removed 24 (10 requested) atoms. Cycle 39: After refmac, R = 0.1774 (Rfree = 0.000) for 4476 atoms. Found 9 (21 requested) and removed 19 (10 requested) atoms. Cycle 40: After refmac, R = 0.1823 (Rfree = 0.000) for 4460 atoms. Found 11 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.80 Search for helices and strands: 0 residues in 0 chains, 4575 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4588 seeds are put forward Round 1: 190 peptides, 41 chains. Longest chain 8 peptides. Score 0.243 Round 2: 211 peptides, 43 chains. Longest chain 8 peptides. Score 0.278 Round 3: 236 peptides, 43 chains. Longest chain 10 peptides. Score 0.342 Round 4: 229 peptides, 42 chains. Longest chain 10 peptides. Score 0.336 Round 5: 234 peptides, 43 chains. Longest chain 12 peptides. Score 0.337 Taking the results from Round 3 Chains 43, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 10057 restraints for refining 4515 atoms. 9328 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1890 (Rfree = 0.000) for 4515 atoms. Found 16 (21 requested) and removed 25 (10 requested) atoms. Cycle 42: After refmac, R = 0.1660 (Rfree = 0.000) for 4491 atoms. Found 10 (21 requested) and removed 19 (10 requested) atoms. Cycle 43: After refmac, R = 0.1806 (Rfree = 0.000) for 4475 atoms. Found 15 (21 requested) and removed 19 (10 requested) atoms. Cycle 44: After refmac, R = 0.1900 (Rfree = 0.000) for 4459 atoms. Found 12 (21 requested) and removed 21 (10 requested) atoms. Cycle 45: After refmac, R = 0.2011 (Rfree = 0.000) for 4444 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.81 Search for helices and strands: 0 residues in 0 chains, 4597 seeds are put forward NCS extension: 0 residues added, 4597 seeds are put forward Round 1: 148 peptides, 35 chains. Longest chain 7 peptides. Score 0.192 Round 2: 194 peptides, 41 chains. Longest chain 13 peptides. Score 0.254 Round 3: 188 peptides, 39 chains. Longest chain 9 peptides. Score 0.261 Round 4: 185 peptides, 37 chains. Longest chain 9 peptides. Score 0.276 Round 5: 181 peptides, 37 chains. Longest chain 8 peptides. Score 0.265 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 148, 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 2op5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6261 reflections ( 99.73 % complete ) and 10015 restraints for refining 4416 atoms. 9460 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1883 (Rfree = 0.000) for 4416 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1748 (Rfree = 0.000) for 4382 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1904 (Rfree = 0.000) for 4363 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2065 (Rfree = 0.000) for 4350 atoms. TimeTaking 52.87