Mon 24 Dec 01:07:24 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 1vll-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-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/1vll-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-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 01:07:28 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/1vll-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-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 396 and 0 Target number of residues in the AU: 396 Target solvent content: 0.6989 Checking the provided sequence file Detected sequence length: 334 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 668 Adjusted target solvent content: 0.49 Input MTZ file: 1vll-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: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5344 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: 76.441 4.000 Wilson plot Bfac: 121.02 6431 reflections ( 99.95 % complete ) and 0 restraints for refining 5910 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3769 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3501 (Rfree = 0.000) for 5910 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.17 4.23 Search for helices and strands: 0 residues in 0 chains, 6010 seeds are put forward NCS extension: 0 residues added, 6010 seeds are put forward Round 1: 202 peptides, 41 chains. Longest chain 11 peptides. Score 0.274 Round 2: 284 peptides, 47 chains. Longest chain 12 peptides. Score 0.411 Round 3: 295 peptides, 47 chains. Longest chain 13 peptides. Score 0.435 Round 4: 309 peptides, 47 chains. Longest chain 14 peptides. Score 0.465 Round 5: 328 peptides, 45 chains. Longest chain 17 peptides. Score 0.522 Taking the results from Round 5 Chains 47, Residues 283, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11437 restraints for refining 4826 atoms. 10278 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2927 (Rfree = 0.000) for 4826 atoms. Found 5 (22 requested) and removed 35 (11 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2731 (Rfree = 0.000) for 4710 atoms. Found 4 (22 requested) and removed 31 (11 requested) atoms. Cycle 3: After refmac, R = 0.2255 (Rfree = 0.000) for 4619 atoms. Found 1 (22 requested) and removed 24 (11 requested) atoms. Cycle 4: After refmac, R = 0.2192 (Rfree = 0.000) for 4567 atoms. Found 2 (21 requested) and removed 23 (10 requested) atoms. Cycle 5: After refmac, R = 0.2376 (Rfree = 0.000) for 4534 atoms. Found 0 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.13 4.19 Search for helices and strands: 0 residues in 0 chains, 4685 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 4712 seeds are put forward Round 1: 281 peptides, 56 chains. Longest chain 10 peptides. Score 0.314 Round 2: 325 peptides, 47 chains. Longest chain 16 peptides. Score 0.498 Round 3: 336 peptides, 51 chains. Longest chain 16 peptides. Score 0.485 Round 4: 336 peptides, 43 chains. Longest chain 17 peptides. Score 0.554 Round 5: 335 peptides, 43 chains. Longest chain 22 peptides. Score 0.552 Taking the results from Round 4 Chains 43, Residues 293, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6431 reflections ( 99.95 % complete ) and 10858 restraints for refining 4655 atoms. 9729 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2528 (Rfree = 0.000) for 4655 atoms. Found 9 (22 requested) and removed 38 (11 requested) atoms. Cycle 7: After refmac, R = 0.2651 (Rfree = 0.000) for 4586 atoms. Found 17 (21 requested) and removed 37 (10 requested) atoms. Cycle 8: After refmac, R = 0.2513 (Rfree = 0.000) for 4544 atoms. Found 9 (21 requested) and removed 32 (10 requested) atoms. Cycle 9: After refmac, R = 0.2566 (Rfree = 0.000) for 4495 atoms. Found 18 (21 requested) and removed 26 (10 requested) atoms. Cycle 10: After refmac, R = 0.2421 (Rfree = 0.000) for 4469 atoms. Found 12 (21 requested) and removed 26 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.09 4.14 Search for helices and strands: 0 residues in 0 chains, 4649 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4665 seeds are put forward Round 1: 254 peptides, 51 chains. Longest chain 9 peptides. Score 0.299 Round 2: 295 peptides, 47 chains. Longest chain 14 peptides. Score 0.435 Round 3: 314 peptides, 47 chains. Longest chain 19 peptides. Score 0.476 Round 4: 296 peptides, 45 chains. Longest chain 13 peptides. Score 0.456 Round 5: 323 peptides, 49 chains. Longest chain 20 peptides. Score 0.476 Taking the results from Round 5 Chains 51, Residues 274, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10965 restraints for refining 4767 atoms. 9825 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2803 (Rfree = 0.000) for 4767 atoms. Found 15 (22 requested) and removed 65 (11 requested) atoms. Cycle 12: After refmac, R = 0.2494 (Rfree = 0.000) for 4687 atoms. Found 7 (22 requested) and removed 36 (11 requested) atoms. Cycle 13: After refmac, R = 0.2309 (Rfree = 0.000) for 4632 atoms. Found 12 (22 requested) and removed 27 (11 requested) atoms. Cycle 14: After refmac, R = 0.2226 (Rfree = 0.000) for 4595 atoms. Found 3 (21 requested) and removed 30 (10 requested) atoms. Cycle 15: After refmac, R = 0.2246 (Rfree = 0.000) for 4551 atoms. Found 8 (21 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.07 4.12 Search for helices and strands: 0 residues in 0 chains, 4694 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 4721 seeds are put forward Round 1: 244 peptides, 48 chains. Longest chain 9 peptides. Score 0.306 Round 2: 312 peptides, 51 chains. Longest chain 15 peptides. Score 0.435 Round 3: 309 peptides, 45 chains. Longest chain 16 peptides. Score 0.484 Round 4: 323 peptides, 49 chains. Longest chain 15 peptides. Score 0.476 Round 5: 327 peptides, 47 chains. Longest chain 17 peptides. Score 0.502 Taking the results from Round 5 Chains 48, Residues 280, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10789 restraints for refining 4793 atoms. 9606 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2515 (Rfree = 0.000) for 4793 atoms. Found 8 (22 requested) and removed 45 (11 requested) atoms. Cycle 17: After refmac, R = 0.2369 (Rfree = 0.000) for 4719 atoms. Found 8 (22 requested) and removed 30 (11 requested) atoms. Cycle 18: After refmac, R = 0.2092 (Rfree = 0.000) for 4670 atoms. Found 5 (22 requested) and removed 19 (11 requested) atoms. Cycle 19: After refmac, R = 0.2101 (Rfree = 0.000) for 4642 atoms. Found 2 (22 requested) and removed 15 (11 requested) atoms. Cycle 20: After refmac, R = 0.2109 (Rfree = 0.000) for 4618 atoms. Found 1 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.11 4.17 Search for helices and strands: 0 residues in 0 chains, 4753 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 4778 seeds are put forward Round 1: 260 peptides, 47 chains. Longest chain 12 peptides. Score 0.356 Round 2: 280 peptides, 47 chains. Longest chain 16 peptides. Score 0.402 Round 3: 284 peptides, 46 chains. Longest chain 14 peptides. Score 0.421 Round 4: 277 peptides, 44 chains. Longest chain 18 peptides. Score 0.425 Round 5: 281 peptides, 45 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 4 Chains 45, Residues 233, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11315 restraints for refining 4807 atoms. 10390 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2691 (Rfree = 0.000) for 4807 atoms. Found 16 (22 requested) and removed 43 (11 requested) atoms. Cycle 22: After refmac, R = 0.2418 (Rfree = 0.000) for 4755 atoms. Found 15 (22 requested) and removed 36 (11 requested) atoms. Cycle 23: After refmac, R = 0.2233 (Rfree = 0.000) for 4710 atoms. Found 6 (22 requested) and removed 30 (11 requested) atoms. Cycle 24: After refmac, R = 0.2325 (Rfree = 0.000) for 4669 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 25: After refmac, R = 0.2231 (Rfree = 0.000) for 4655 atoms. Found 17 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.07 4.12 Search for helices and strands: 0 residues in 0 chains, 4841 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 4877 seeds are put forward Round 1: 213 peptides, 45 chains. Longest chain 8 peptides. Score 0.259 Round 2: 264 peptides, 49 chains. Longest chain 11 peptides. Score 0.345 Round 3: 270 peptides, 45 chains. Longest chain 12 peptides. Score 0.399 Round 4: 268 peptides, 44 chains. Longest chain 12 peptides. Score 0.405 Round 5: 277 peptides, 45 chains. Longest chain 15 peptides. Score 0.415 Taking the results from Round 5 Chains 45, Residues 232, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11187 restraints for refining 4813 atoms. 10278 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2273 (Rfree = 0.000) for 4813 atoms. Found 7 (22 requested) and removed 51 (11 requested) atoms. Cycle 27: After refmac, R = 0.2374 (Rfree = 0.000) for 4733 atoms. Found 10 (22 requested) and removed 31 (11 requested) atoms. Cycle 28: After refmac, R = 0.2397 (Rfree = 0.000) for 4679 atoms. Found 18 (22 requested) and removed 31 (11 requested) atoms. Cycle 29: After refmac, R = 0.2422 (Rfree = 0.000) for 4637 atoms. Found 20 (22 requested) and removed 30 (11 requested) atoms. Cycle 30: After refmac, R = 0.2273 (Rfree = 0.000) for 4597 atoms. Found 12 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.08 4.13 Search for helices and strands: 0 residues in 0 chains, 4732 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4750 seeds are put forward Round 1: 213 peptides, 46 chains. Longest chain 8 peptides. Score 0.248 Round 2: 251 peptides, 44 chains. Longest chain 11 peptides. Score 0.365 Round 3: 253 peptides, 42 chains. Longest chain 11 peptides. Score 0.390 Round 4: 274 peptides, 46 chains. Longest chain 12 peptides. Score 0.398 Round 5: 277 peptides, 43 chains. Longest chain 17 peptides. Score 0.435 Taking the results from Round 5 Chains 44, Residues 234, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10692 restraints for refining 4731 atoms. 9710 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2369 (Rfree = 0.000) for 4731 atoms. Found 7 (22 requested) and removed 49 (11 requested) atoms. Cycle 32: After refmac, R = 0.2357 (Rfree = 0.000) for 4662 atoms. Found 14 (22 requested) and removed 20 (11 requested) atoms. Cycle 33: After refmac, R = 0.2183 (Rfree = 0.000) for 4638 atoms. Found 6 (22 requested) and removed 32 (11 requested) atoms. Cycle 34: After refmac, R = 0.2286 (Rfree = 0.000) for 4592 atoms. Found 4 (21 requested) and removed 29 (10 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2050 (Rfree = 0.000) for 4555 atoms. Found 2 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.06 4.11 Search for helices and strands: 0 residues in 0 chains, 4678 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4693 seeds are put forward Round 1: 205 peptides, 43 chains. Longest chain 10 peptides. Score 0.260 Round 2: 241 peptides, 44 chains. Longest chain 14 peptides. Score 0.341 Round 3: 246 peptides, 42 chains. Longest chain 13 peptides. Score 0.374 Round 4: 250 peptides, 40 chains. Longest chain 19 peptides. Score 0.404 Round 5: 257 peptides, 42 chains. Longest chain 12 peptides. Score 0.399 Taking the results from Round 4 Chains 40, Residues 210, Estimated correctness of the model 0.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10799 restraints for refining 4728 atoms. 9889 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2340 (Rfree = 0.000) for 4728 atoms. Found 17 (22 requested) and removed 38 (11 requested) atoms. Cycle 37: After refmac, R = 0.2331 (Rfree = 0.000) for 4680 atoms. Found 19 (22 requested) and removed 32 (11 requested) atoms. Cycle 38: After refmac, R = 0.2294 (Rfree = 0.000) for 4634 atoms. Found 15 (22 requested) and removed 23 (11 requested) atoms. Cycle 39: After refmac, R = 0.1821 (Rfree = 0.000) for 4606 atoms. Found 6 (21 requested) and removed 18 (10 requested) atoms. Cycle 40: After refmac, R = 0.1657 (Rfree = 0.000) for 4586 atoms. Found 5 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.08 4.13 Search for helices and strands: 0 residues in 0 chains, 4694 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4708 seeds are put forward Round 1: 185 peptides, 41 chains. Longest chain 8 peptides. Score 0.228 Round 2: 238 peptides, 46 chains. Longest chain 11 peptides. Score 0.312 Round 3: 246 peptides, 43 chains. Longest chain 12 peptides. Score 0.363 Round 4: 252 peptides, 44 chains. Longest chain 12 peptides. Score 0.367 Round 5: 238 peptides, 39 chains. Longest chain 12 peptides. Score 0.386 Taking the results from Round 5 Chains 39, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10970 restraints for refining 4668 atoms. 10213 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2361 (Rfree = 0.000) for 4668 atoms. Found 11 (22 requested) and removed 46 (11 requested) atoms. Cycle 42: After refmac, R = 0.2276 (Rfree = 0.000) for 4607 atoms. Found 9 (22 requested) and removed 25 (11 requested) atoms. Cycle 43: After refmac, R = 0.2320 (Rfree = 0.000) for 4565 atoms. Found 14 (21 requested) and removed 23 (10 requested) atoms. Cycle 44: After refmac, R = 0.2175 (Rfree = 0.000) for 4533 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Cycle 45: After refmac, R = 0.2302 (Rfree = 0.000) for 4514 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.08 4.13 Search for helices and strands: 0 residues in 0 chains, 4626 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4640 seeds are put forward Round 1: 148 peptides, 34 chains. Longest chain 6 peptides. Score 0.204 Round 2: 181 peptides, 36 chains. Longest chain 10 peptides. Score 0.275 Round 3: 195 peptides, 35 chains. Longest chain 10 peptides. Score 0.323 Round 4: 198 peptides, 33 chains. Longest chain 11 peptides. Score 0.353 Round 5: 195 peptides, 33 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 165, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vll-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6431 reflections ( 99.95 % complete ) and 10001 restraints for refining 4433 atoms. 9342 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2242 (Rfree = 0.000) for 4433 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2232 (Rfree = 0.000) for 4409 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2201 (Rfree = 0.000) for 4383 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2294 (Rfree = 0.000) for 4357 atoms. TimeTaking 45.95