Sun 23 Dec 23:59:47 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 2pgc-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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/2pgc-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 ============================================================ Sun 23 Dec 23:59:51 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/2pgc-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 708 and 0 Target number of residues in the AU: 708 Target solvent content: 0.6719 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8280 target number of atoms Had to go as low as 0.80 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: 98.043 4.000 Wilson plot Bfac: 93.78 10366 reflections ( 99.41 % complete ) and 0 restraints for refining 9140 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3463 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3329 (Rfree = 0.000) for 9140 atoms. Found 43 (43 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.88 3.78 Search for helices and strands: 0 residues in 0 chains, 9338 seeds are put forward NCS extension: 0 residues added, 9338 seeds are put forward Round 1: 323 peptides, 64 chains. Longest chain 12 peptides. Score 0.283 Round 2: 426 peptides, 73 chains. Longest chain 13 peptides. Score 0.380 Round 3: 493 peptides, 73 chains. Longest chain 22 peptides. Score 0.471 Round 4: 507 peptides, 72 chains. Longest chain 23 peptides. Score 0.494 Round 5: 529 peptides, 73 chains. Longest chain 24 peptides. Score 0.515 Taking the results from Round 5 Chains 73, Residues 456, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17511 restraints for refining 7470 atoms. 15729 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2627 (Rfree = 0.000) for 7470 atoms. Found 20 (35 requested) and removed 40 (17 requested) atoms. Cycle 2: After refmac, R = 0.2356 (Rfree = 0.000) for 7322 atoms. Found 19 (35 requested) and removed 33 (17 requested) atoms. Cycle 3: After refmac, R = 0.2124 (Rfree = 0.000) for 7252 atoms. Found 12 (34 requested) and removed 25 (17 requested) atoms. Cycle 4: After refmac, R = 0.2055 (Rfree = 0.000) for 7213 atoms. Found 5 (34 requested) and removed 27 (17 requested) atoms. Cycle 5: After refmac, R = 0.2069 (Rfree = 0.000) for 7177 atoms. Found 15 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 7462 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 7488 seeds are put forward Round 1: 427 peptides, 78 chains. Longest chain 12 peptides. Score 0.351 Round 2: 507 peptides, 74 chains. Longest chain 24 peptides. Score 0.483 Round 3: 534 peptides, 75 chains. Longest chain 19 peptides. Score 0.510 Round 4: 556 peptides, 70 chains. Longest chain 25 peptides. Score 0.562 Round 5: 540 peptides, 71 chains. Longest chain 28 peptides. Score 0.539 Taking the results from Round 4 Chains 70, Residues 486, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17293 restraints for refining 7478 atoms. 15393 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2218 (Rfree = 0.000) for 7478 atoms. Found 26 (35 requested) and removed 52 (17 requested) atoms. Cycle 7: After refmac, R = 0.2019 (Rfree = 0.000) for 7371 atoms. Found 7 (35 requested) and removed 24 (17 requested) atoms. Cycle 8: After refmac, R = 0.2000 (Rfree = 0.000) for 7333 atoms. Found 4 (34 requested) and removed 21 (17 requested) atoms. Cycle 9: After refmac, R = 0.1990 (Rfree = 0.000) for 7312 atoms. Found 1 (34 requested) and removed 17 (17 requested) atoms. Cycle 10: After refmac, R = 0.1990 (Rfree = 0.000) for 7295 atoms. Found 5 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 7517 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 7543 seeds are put forward Round 1: 462 peptides, 81 chains. Longest chain 23 peptides. Score 0.382 Round 2: 528 peptides, 71 chains. Longest chain 23 peptides. Score 0.525 Round 3: 540 peptides, 64 chains. Longest chain 29 peptides. Score 0.574 Round 4: 512 peptides, 58 chains. Longest chain 25 peptides. Score 0.574 Round 5: 509 peptides, 61 chains. Longest chain 27 peptides. Score 0.555 Taking the results from Round 4 Chains 59, Residues 454, Estimated correctness of the model 0.0 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17009 restraints for refining 7477 atoms. 15093 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2222 (Rfree = 0.000) for 7477 atoms. Found 17 (35 requested) and removed 21 (17 requested) atoms. Cycle 12: After refmac, R = 0.2143 (Rfree = 0.000) for 7434 atoms. Found 10 (35 requested) and removed 17 (17 requested) atoms. Cycle 13: After refmac, R = 0.2121 (Rfree = 0.000) for 7420 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 14: After refmac, R = 0.2111 (Rfree = 0.000) for 7400 atoms. Found 2 (35 requested) and removed 18 (17 requested) atoms. Cycle 15: After refmac, R = 0.2093 (Rfree = 0.000) for 7381 atoms. Found 1 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.86 3.76 Search for helices and strands: 0 residues in 0 chains, 7618 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 7641 seeds are put forward Round 1: 422 peptides, 74 chains. Longest chain 15 peptides. Score 0.368 Round 2: 496 peptides, 72 chains. Longest chain 20 peptides. Score 0.480 Round 3: 516 peptides, 73 chains. Longest chain 17 peptides. Score 0.499 Round 4: 490 peptides, 65 chains. Longest chain 21 peptides. Score 0.511 Round 5: 489 peptides, 70 chains. Longest chain 19 peptides. Score 0.483 Taking the results from Round 4 Chains 65, Residues 425, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17859 restraints for refining 7478 atoms. 16224 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2322 (Rfree = 0.000) for 7478 atoms. Found 20 (35 requested) and removed 32 (17 requested) atoms. Cycle 17: After refmac, R = 0.2241 (Rfree = 0.000) for 7370 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 18: After refmac, R = 0.2100 (Rfree = 0.000) for 7329 atoms. Found 27 (35 requested) and removed 20 (17 requested) atoms. Cycle 19: After refmac, R = 0.1764 (Rfree = 0.000) for 7300 atoms. Found 6 (34 requested) and removed 23 (17 requested) atoms. Cycle 20: After refmac, R = 0.1753 (Rfree = 0.000) for 7256 atoms. Found 5 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.90 3.80 Search for helices and strands: 0 residues in 0 chains, 7498 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 7527 seeds are put forward Round 1: 390 peptides, 75 chains. Longest chain 11 peptides. Score 0.315 Round 2: 459 peptides, 76 chains. Longest chain 15 peptides. Score 0.408 Round 3: 459 peptides, 69 chains. Longest chain 18 peptides. Score 0.450 Round 4: 478 peptides, 75 chains. Longest chain 15 peptides. Score 0.440 Round 5: 502 peptides, 68 chains. Longest chain 21 peptides. Score 0.510 Taking the results from Round 5 Chains 69, Residues 434, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17489 restraints for refining 7478 atoms. 15746 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2419 (Rfree = 0.000) for 7478 atoms. Found 35 (35 requested) and removed 117 (17 requested) atoms. Cycle 22: After refmac, R = 0.2157 (Rfree = 0.000) for 7309 atoms. Found 35 (35 requested) and removed 35 (17 requested) atoms. Cycle 23: After refmac, R = 0.2072 (Rfree = 0.000) for 7253 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. Cycle 24: After refmac, R = 0.2137 (Rfree = 0.000) for 7228 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 25: After refmac, R = 0.1942 (Rfree = 0.000) for 7206 atoms. Found 22 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 7475 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 7496 seeds are put forward Round 1: 364 peptides, 74 chains. Longest chain 14 peptides. Score 0.281 Round 2: 455 peptides, 76 chains. Longest chain 22 peptides. Score 0.403 Round 3: 462 peptides, 76 chains. Longest chain 15 peptides. Score 0.412 Round 4: 460 peptides, 77 chains. Longest chain 15 peptides. Score 0.404 Round 5: 473 peptides, 76 chains. Longest chain 16 peptides. Score 0.427 Taking the results from Round 5 Chains 76, Residues 397, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17654 restraints for refining 7431 atoms. 16132 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2567 (Rfree = 0.000) for 7431 atoms. Found 35 (35 requested) and removed 48 (17 requested) atoms. Cycle 27: After refmac, R = 0.2253 (Rfree = 0.000) for 7325 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 28: After refmac, R = 0.2038 (Rfree = 0.000) for 7253 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 29: After refmac, R = 0.1615 (Rfree = 0.000) for 7231 atoms. Found 14 (34 requested) and removed 20 (17 requested) atoms. Cycle 30: After refmac, R = 0.1597 (Rfree = 0.000) for 7202 atoms. Found 26 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 7441 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7459 seeds are put forward Round 1: 374 peptides, 81 chains. Longest chain 9 peptides. Score 0.250 Round 2: 443 peptides, 81 chains. Longest chain 12 peptides. Score 0.355 Round 3: 419 peptides, 80 chains. Longest chain 12 peptides. Score 0.326 Round 4: 407 peptides, 72 chains. Longest chain 16 peptides. Score 0.359 Round 5: 432 peptides, 77 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 5 Chains 77, Residues 355, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17768 restraints for refining 7450 atoms. 16413 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2360 (Rfree = 0.000) for 7450 atoms. Found 35 (35 requested) and removed 60 (17 requested) atoms. Cycle 32: After refmac, R = 0.2094 (Rfree = 0.000) for 7356 atoms. Found 35 (35 requested) and removed 41 (17 requested) atoms. Cycle 33: After refmac, R = 0.2146 (Rfree = 0.000) for 7307 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 34: After refmac, R = 0.2115 (Rfree = 0.000) for 7278 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 35: After refmac, R = 0.2062 (Rfree = 0.000) for 7251 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 7445 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7459 seeds are put forward Round 1: 278 peptides, 60 chains. Longest chain 8 peptides. Score 0.236 Round 2: 365 peptides, 67 chains. Longest chain 15 peptides. Score 0.329 Round 3: 377 peptides, 72 chains. Longest chain 11 peptides. Score 0.314 Round 4: 377 peptides, 66 chains. Longest chain 16 peptides. Score 0.353 Round 5: 376 peptides, 67 chains. Longest chain 15 peptides. Score 0.345 Taking the results from Round 4 Chains 66, Residues 311, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17157 restraints for refining 7268 atoms. 15924 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2420 (Rfree = 0.000) for 7268 atoms. Found 34 (34 requested) and removed 48 (17 requested) atoms. Cycle 37: After refmac, R = 0.2153 (Rfree = 0.000) for 7181 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 38: After refmac, R = 0.2104 (Rfree = 0.000) for 7138 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 39: After refmac, R = 0.1593 (Rfree = 0.000) for 7111 atoms. Found 9 (33 requested) and removed 17 (16 requested) atoms. Cycle 40: After refmac, R = 0.1463 (Rfree = 0.000) for 7093 atoms. Found 6 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 7255 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 7280 seeds are put forward Round 1: 283 peptides, 63 chains. Longest chain 7 peptides. Score 0.223 Round 2: 351 peptides, 69 chains. Longest chain 9 peptides. Score 0.294 Round 3: 369 peptides, 70 chains. Longest chain 10 peptides. Score 0.315 Round 4: 373 peptides, 67 chains. Longest chain 12 peptides. Score 0.341 Round 5: 391 peptides, 66 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 5 Chains 67, Residues 325, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 16807 restraints for refining 7230 atoms. 15549 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2217 (Rfree = 0.000) for 7230 atoms. Found 34 (34 requested) and removed 66 (17 requested) atoms. Cycle 42: After refmac, R = 0.2197 (Rfree = 0.000) for 7166 atoms. Found 34 (34 requested) and removed 38 (17 requested) atoms. Cycle 43: After refmac, R = 0.1645 (Rfree = 0.000) for 7123 atoms. Found 12 (34 requested) and removed 29 (17 requested) atoms. Cycle 44: After refmac, R = 0.1928 (Rfree = 0.000) for 7081 atoms. Found 33 (33 requested) and removed 29 (16 requested) atoms. Cycle 45: After refmac, R = 0.1526 (Rfree = 0.000) for 7072 atoms. Found 17 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 7228 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 7244 seeds are put forward Round 1: 300 peptides, 63 chains. Longest chain 8 peptides. Score 0.252 Round 2: 354 peptides, 69 chains. Longest chain 13 peptides. Score 0.299 Round 3: 355 peptides, 66 chains. Longest chain 12 peptides. Score 0.320 Round 4: 382 peptides, 69 chains. Longest chain 15 peptides. Score 0.341 Round 5: 398 peptides, 68 chains. Longest chain 18 peptides. Score 0.371 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 68, Residues 330, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2pgc-4_warpNtrace.pdb as input Building loops using Loopy2018 68 chains (330 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10366 reflections ( 99.41 % complete ) and 17143 restraints for refining 7337 atoms. 15877 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1842 (Rfree = 0.000) for 7337 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1999 (Rfree = 0.000) for 7284 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2260 (Rfree = 0.000) for 7250 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1576 (Rfree = 0.000) for 7194 atoms. TimeTaking 68.35