Mon 24 Dec 07:51:19 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 2aml-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aml-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aml-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.4-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/2aml-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.4-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 07:51:24 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/2aml-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.4-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 474 and 0 Target number of residues in the AU: 474 Target solvent content: 0.6261 Checking the provided sequence file Detected sequence length: 373 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 746 Adjusted target solvent content: 0.41 Input MTZ file: 2aml-3.4-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: 19 Cell parameters: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 5968 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: 77.491 3.400 Wilson plot Bfac: 64.20 9931 reflections ( 99.79 % complete ) and 0 restraints for refining 6607 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3256 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3162 (Rfree = 0.000) for 6607 atoms. Found 49 (49 requested) and removed 97 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 6708 seeds are put forward NCS extension: 0 residues added, 6708 seeds are put forward Round 1: 273 peptides, 62 chains. Longest chain 8 peptides. Score 0.234 Round 2: 360 peptides, 69 chains. Longest chain 11 peptides. Score 0.377 Round 3: 364 peptides, 59 chains. Longest chain 16 peptides. Score 0.479 Round 4: 384 peptides, 64 chains. Longest chain 18 peptides. Score 0.476 Round 5: 389 peptides, 63 chains. Longest chain 15 peptides. Score 0.495 Taking the results from Round 5 Chains 64, Residues 326, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12248 restraints for refining 5427 atoms. 10972 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2669 (Rfree = 0.000) for 5427 atoms. Found 33 (40 requested) and removed 52 (20 requested) atoms. Cycle 2: After refmac, R = 0.2375 (Rfree = 0.000) for 5342 atoms. Found 28 (40 requested) and removed 37 (20 requested) atoms. Cycle 3: After refmac, R = 0.2293 (Rfree = 0.000) for 5295 atoms. Found 23 (40 requested) and removed 39 (20 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1873 (Rfree = 0.000) for 5260 atoms. Found 17 (39 requested) and removed 23 (19 requested) atoms. Cycle 5: After refmac, R = 0.1741 (Rfree = 0.000) for 5246 atoms. Found 2 (39 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.65 Search for helices and strands: 0 residues in 0 chains, 5435 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5452 seeds are put forward Round 1: 324 peptides, 64 chains. Longest chain 13 peptides. Score 0.342 Round 2: 366 peptides, 61 chains. Longest chain 15 peptides. Score 0.465 Round 3: 379 peptides, 62 chains. Longest chain 19 peptides. Score 0.484 Round 4: 380 peptides, 59 chains. Longest chain 17 peptides. Score 0.512 Round 5: 385 peptides, 54 chains. Longest chain 19 peptides. Score 0.563 Taking the results from Round 5 Chains 54, Residues 331, Estimated correctness of the model 16.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12299 restraints for refining 5382 atoms. 11029 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2471 (Rfree = 0.000) for 5382 atoms. Found 40 (40 requested) and removed 50 (20 requested) atoms. Cycle 7: After refmac, R = 0.2391 (Rfree = 0.000) for 5351 atoms. Found 40 (40 requested) and removed 34 (20 requested) atoms. Cycle 8: After refmac, R = 0.2173 (Rfree = 0.000) for 5337 atoms. Found 40 (40 requested) and removed 34 (20 requested) atoms. Cycle 9: After refmac, R = 0.2079 (Rfree = 0.000) for 5321 atoms. Found 39 (40 requested) and removed 29 (20 requested) atoms. Cycle 10: After refmac, R = 0.2085 (Rfree = 0.000) for 5321 atoms. Found 29 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.68 Search for helices and strands: 0 residues in 0 chains, 5562 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5585 seeds are put forward Round 1: 318 peptides, 57 chains. Longest chain 16 peptides. Score 0.397 Round 2: 372 peptides, 59 chains. Longest chain 18 peptides. Score 0.496 Round 3: 365 peptides, 54 chains. Longest chain 20 peptides. Score 0.525 Round 4: 344 peptides, 52 chains. Longest chain 20 peptides. Score 0.501 Round 5: 350 peptides, 49 chains. Longest chain 20 peptides. Score 0.539 Taking the results from Round 5 Chains 49, Residues 301, Estimated correctness of the model 7.5 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12467 restraints for refining 5426 atoms. 11257 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2496 (Rfree = 0.000) for 5426 atoms. Found 40 (40 requested) and removed 47 (20 requested) atoms. Cycle 12: After refmac, R = 0.2128 (Rfree = 0.000) for 5378 atoms. Found 40 (40 requested) and removed 38 (20 requested) atoms. Cycle 13: After refmac, R = 0.2091 (Rfree = 0.000) for 5364 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 14: After refmac, R = 0.2033 (Rfree = 0.000) for 5363 atoms. Found 40 (40 requested) and removed 29 (20 requested) atoms. Cycle 15: After refmac, R = 0.1644 (Rfree = 0.000) for 5364 atoms. Found 17 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.76 Search for helices and strands: 0 residues in 0 chains, 5597 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5613 seeds are put forward Round 1: 297 peptides, 55 chains. Longest chain 12 peptides. Score 0.368 Round 2: 334 peptides, 51 chains. Longest chain 25 peptides. Score 0.489 Round 3: 348 peptides, 53 chains. Longest chain 17 peptides. Score 0.500 Round 4: 341 peptides, 53 chains. Longest chain 20 peptides. Score 0.486 Round 5: 352 peptides, 48 chains. Longest chain 21 peptides. Score 0.551 Taking the results from Round 5 Chains 50, Residues 304, Estimated correctness of the model 11.9 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12384 restraints for refining 5427 atoms. 11177 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2155 (Rfree = 0.000) for 5427 atoms. Found 40 (40 requested) and removed 27 (20 requested) atoms. Cycle 17: After refmac, R = 0.2205 (Rfree = 0.000) for 5421 atoms. Found 41 (41 requested) and removed 32 (20 requested) atoms. Cycle 18: After refmac, R = 0.2096 (Rfree = 0.000) for 5418 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 19: After refmac, R = 0.2042 (Rfree = 0.000) for 5417 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 20: After refmac, R = 0.1964 (Rfree = 0.000) for 5407 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.66 Search for helices and strands: 0 residues in 0 chains, 5627 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 5658 seeds are put forward Round 1: 281 peptides, 55 chains. Longest chain 11 peptides. Score 0.329 Round 2: 319 peptides, 53 chains. Longest chain 15 peptides. Score 0.438 Round 3: 327 peptides, 50 chains. Longest chain 16 peptides. Score 0.484 Round 4: 338 peptides, 50 chains. Longest chain 20 peptides. Score 0.506 Round 5: 338 peptides, 47 chains. Longest chain 16 peptides. Score 0.533 Taking the results from Round 5 Chains 50, Residues 291, Estimated correctness of the model 5.3 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12265 restraints for refining 5427 atoms. 11065 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2125 (Rfree = 0.000) for 5427 atoms. Found 40 (40 requested) and removed 34 (20 requested) atoms. Cycle 22: After refmac, R = 0.2090 (Rfree = 0.000) for 5417 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 23: After refmac, R = 0.2032 (Rfree = 0.000) for 5413 atoms. Found 41 (41 requested) and removed 33 (20 requested) atoms. Cycle 24: After refmac, R = 0.1899 (Rfree = 0.000) for 5411 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 25: After refmac, R = 0.1794 (Rfree = 0.000) for 5413 atoms. Found 40 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 5637 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5657 seeds are put forward Round 1: 244 peptides, 48 chains. Longest chain 13 peptides. Score 0.310 Round 2: 277 peptides, 47 chains. Longest chain 15 peptides. Score 0.402 Round 3: 292 peptides, 46 chains. Longest chain 17 peptides. Score 0.446 Round 4: 284 peptides, 41 chains. Longest chain 18 peptides. Score 0.477 Round 5: 292 peptides, 42 chains. Longest chain 19 peptides. Score 0.484 Taking the results from Round 5 Chains 42, Residues 250, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12911 restraints for refining 5426 atoms. 11921 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1931 (Rfree = 0.000) for 5426 atoms. Found 37 (40 requested) and removed 28 (20 requested) atoms. Cycle 27: After refmac, R = 0.1970 (Rfree = 0.000) for 5415 atoms. Found 41 (41 requested) and removed 29 (20 requested) atoms. Cycle 28: After refmac, R = 0.1549 (Rfree = 0.000) for 5421 atoms. Found 19 (40 requested) and removed 23 (20 requested) atoms. Cycle 29: After refmac, R = 0.1479 (Rfree = 0.000) for 5411 atoms. Found 15 (40 requested) and removed 23 (20 requested) atoms. Cycle 30: After refmac, R = 0.1457 (Rfree = 0.000) for 5396 atoms. Found 9 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 5547 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 5576 seeds are put forward Round 1: 259 peptides, 52 chains. Longest chain 11 peptides. Score 0.305 Round 2: 284 peptides, 47 chains. Longest chain 16 peptides. Score 0.418 Round 3: 293 peptides, 46 chains. Longest chain 16 peptides. Score 0.448 Round 4: 311 peptides, 44 chains. Longest chain 21 peptides. Score 0.505 Round 5: 290 peptides, 41 chains. Longest chain 22 peptides. Score 0.489 Taking the results from Round 4 Chains 48, Residues 267, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12504 restraints for refining 5426 atoms. 11428 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1806 (Rfree = 0.000) for 5426 atoms. Found 35 (40 requested) and removed 28 (20 requested) atoms. Cycle 32: After refmac, R = 0.1750 (Rfree = 0.000) for 5419 atoms. Found 40 (41 requested) and removed 24 (20 requested) atoms. Cycle 33: After refmac, R = 0.1667 (Rfree = 0.000) for 5424 atoms. Found 37 (41 requested) and removed 27 (20 requested) atoms. Cycle 34: After refmac, R = 0.1605 (Rfree = 0.000) for 5424 atoms. Found 32 (41 requested) and removed 23 (20 requested) atoms. Cycle 35: After refmac, R = 0.1467 (Rfree = 0.000) for 5433 atoms. Found 24 (41 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.66 Search for helices and strands: 0 residues in 0 chains, 5626 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5649 seeds are put forward Round 1: 250 peptides, 52 chains. Longest chain 10 peptides. Score 0.282 Round 2: 272 peptides, 48 chains. Longest chain 19 peptides. Score 0.380 Round 3: 280 peptides, 48 chains. Longest chain 19 peptides. Score 0.398 Round 4: 297 peptides, 48 chains. Longest chain 20 peptides. Score 0.437 Round 5: 286 peptides, 51 chains. Longest chain 12 peptides. Score 0.382 Taking the results from Round 4 Chains 50, Residues 249, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12530 restraints for refining 5427 atoms. 11489 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1773 (Rfree = 0.000) for 5427 atoms. Found 33 (40 requested) and removed 26 (20 requested) atoms. Cycle 37: After refmac, R = 0.1672 (Rfree = 0.000) for 5423 atoms. Found 15 (41 requested) and removed 21 (20 requested) atoms. Cycle 38: After refmac, R = 0.1669 (Rfree = 0.000) for 5406 atoms. Found 14 (40 requested) and removed 27 (20 requested) atoms. Cycle 39: After refmac, R = 0.1662 (Rfree = 0.000) for 5392 atoms. Found 26 (40 requested) and removed 23 (20 requested) atoms. Cycle 40: After refmac, R = 0.1697 (Rfree = 0.000) for 5392 atoms. Found 22 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 5572 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5585 seeds are put forward Round 1: 212 peptides, 44 chains. Longest chain 9 peptides. Score 0.270 Round 2: 250 peptides, 38 chains. Longest chain 25 peptides. Score 0.431 Round 3: 253 peptides, 44 chains. Longest chain 13 peptides. Score 0.375 Round 4: 253 peptides, 45 chains. Longest chain 15 peptides. Score 0.365 Round 5: 264 peptides, 46 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 2 Chains 39, Residues 212, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12870 restraints for refining 5427 atoms. 12029 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2127 (Rfree = 0.000) for 5427 atoms. Found 40 (40 requested) and removed 26 (20 requested) atoms. Cycle 42: After refmac, R = 0.1642 (Rfree = 0.000) for 5432 atoms. Found 25 (41 requested) and removed 23 (20 requested) atoms. Cycle 43: After refmac, R = 0.1592 (Rfree = 0.000) for 5429 atoms. Found 21 (41 requested) and removed 22 (20 requested) atoms. Cycle 44: After refmac, R = 0.1554 (Rfree = 0.000) for 5420 atoms. Found 29 (40 requested) and removed 23 (20 requested) atoms. Cycle 45: After refmac, R = 0.1610 (Rfree = 0.000) for 5424 atoms. Found 40 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 5624 seeds are put forward NCS extension: 39 residues added (5 deleted due to clashes), 5663 seeds are put forward Round 1: 226 peptides, 48 chains. Longest chain 9 peptides. Score 0.263 Round 2: 254 peptides, 45 chains. Longest chain 11 peptides. Score 0.367 Round 3: 252 peptides, 41 chains. Longest chain 15 peptides. Score 0.404 Round 4: 262 peptides, 41 chains. Longest chain 14 peptides. Score 0.428 Round 5: 280 peptides, 43 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 237, 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 2aml-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9931 reflections ( 99.79 % complete ) and 12771 restraints for refining 5427 atoms. 11866 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1693 (Rfree = 0.000) for 5427 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1642 (Rfree = 0.000) for 5399 atoms. Found 0 (40 requested) and removed 19 (20 requested) atoms. Cycle 48: After refmac, R = 0.1594 (Rfree = 0.000) for 5377 atoms. Found 0 (40 requested) and removed 15 (20 requested) atoms. Cycle 49: After refmac, R = 0.1567 (Rfree = 0.000) for 5358 atoms. TimeTaking 58.68