Mon 24 Dec 00:31:25 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 2ffj-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.4-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/2ffj-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.4-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 00:31:30 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/2ffj-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.4-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 437 and 0 Target number of residues in the AU: 437 Target solvent content: 0.6475 Checking the provided sequence file Detected sequence length: 300 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 600 Adjusted target solvent content: 0.52 Input MTZ file: 2ffj-3.4-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: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.55 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: 29.898 3.400 Wilson plot Bfac: 76.26 9629 reflections ( 99.03 % complete ) and 0 restraints for refining 5287 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3283 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3407 (Rfree = 0.000) for 5287 atoms. Found 39 (39 requested) and removed 44 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 5419 seeds are put forward NCS extension: 0 residues added, 5419 seeds are put forward Round 1: 242 peptides, 45 chains. Longest chain 11 peptides. Score 0.340 Round 2: 314 peptides, 45 chains. Longest chain 15 peptides. Score 0.508 Round 3: 344 peptides, 43 chains. Longest chain 19 peptides. Score 0.584 Round 4: 355 peptides, 41 chains. Longest chain 23 peptides. Score 0.620 Round 5: 367 peptides, 37 chains. Longest chain 30 peptides. Score 0.670 Taking the results from Round 5 Chains 39, Residues 330, Estimated correctness of the model 49.8 % 3 chains (63 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9015 restraints for refining 4360 atoms. 7498 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2933 (Rfree = 0.000) for 4360 atoms. Found 20 (32 requested) and removed 55 (16 requested) atoms. Cycle 2: After refmac, R = 0.2884 (Rfree = 0.000) for 4212 atoms. Found 22 (32 requested) and removed 37 (16 requested) atoms. Cycle 3: After refmac, R = 0.2808 (Rfree = 0.000) for 4151 atoms. Found 21 (31 requested) and removed 32 (15 requested) atoms. Cycle 4: After refmac, R = 0.2447 (Rfree = 0.000) for 4094 atoms. Found 12 (31 requested) and removed 31 (15 requested) atoms. Cycle 5: After refmac, R = 0.2570 (Rfree = 0.000) for 4058 atoms. Found 13 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.39 Search for helices and strands: 0 residues in 0 chains, 4249 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 4274 seeds are put forward Round 1: 344 peptides, 56 chains. Longest chain 18 peptides. Score 0.469 Round 2: 373 peptides, 43 chains. Longest chain 26 peptides. Score 0.635 Round 3: 378 peptides, 46 chains. Longest chain 25 peptides. Score 0.620 Round 4: 366 peptides, 47 chains. Longest chain 21 peptides. Score 0.592 Round 5: 348 peptides, 40 chains. Longest chain 21 peptides. Score 0.616 Taking the results from Round 2 Chains 45, Residues 330, Estimated correctness of the model 39.7 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 8871 restraints for refining 4257 atoms. 7383 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2766 (Rfree = 0.000) for 4257 atoms. Found 27 (32 requested) and removed 58 (16 requested) atoms. Cycle 7: After refmac, R = 0.2575 (Rfree = 0.000) for 4192 atoms. Found 17 (31 requested) and removed 37 (15 requested) atoms. Cycle 8: After refmac, R = 0.2422 (Rfree = 0.000) for 4148 atoms. Found 19 (31 requested) and removed 29 (15 requested) atoms. Cycle 9: After refmac, R = 0.2424 (Rfree = 0.000) for 4131 atoms. Found 8 (31 requested) and removed 25 (15 requested) atoms. Cycle 10: After refmac, R = 0.2373 (Rfree = 0.000) for 4107 atoms. Found 9 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 4281 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4299 seeds are put forward Round 1: 315 peptides, 48 chains. Longest chain 15 peptides. Score 0.482 Round 2: 339 peptides, 43 chains. Longest chain 24 peptides. Score 0.575 Round 3: 340 peptides, 41 chains. Longest chain 17 peptides. Score 0.594 Round 4: 360 peptides, 42 chains. Longest chain 21 peptides. Score 0.621 Round 5: 340 peptides, 39 chains. Longest chain 24 peptides. Score 0.610 Taking the results from Round 4 Chains 46, Residues 318, Estimated correctness of the model 35.4 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9288 restraints for refining 4364 atoms. 7885 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2800 (Rfree = 0.000) for 4364 atoms. Found 26 (32 requested) and removed 64 (16 requested) atoms. Cycle 12: After refmac, R = 0.2640 (Rfree = 0.000) for 4291 atoms. Found 18 (32 requested) and removed 35 (16 requested) atoms. Cycle 13: After refmac, R = 0.2485 (Rfree = 0.000) for 4259 atoms. Found 9 (32 requested) and removed 26 (16 requested) atoms. Cycle 14: After refmac, R = 0.2424 (Rfree = 0.000) for 4234 atoms. Found 12 (32 requested) and removed 23 (16 requested) atoms. Cycle 15: After refmac, R = 0.2377 (Rfree = 0.000) for 4218 atoms. Found 6 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 4385 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 4402 seeds are put forward Round 1: 316 peptides, 50 chains. Longest chain 15 peptides. Score 0.465 Round 2: 351 peptides, 44 chains. Longest chain 24 peptides. Score 0.589 Round 3: 348 peptides, 47 chains. Longest chain 20 peptides. Score 0.558 Round 4: 357 peptides, 42 chains. Longest chain 18 peptides. Score 0.616 Round 5: 362 peptides, 44 chains. Longest chain 34 peptides. Score 0.608 Taking the results from Round 4 Chains 43, Residues 315, Estimated correctness of the model 33.8 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9596 restraints for refining 4365 atoms. 8275 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2654 (Rfree = 0.000) for 4365 atoms. Found 29 (32 requested) and removed 35 (16 requested) atoms. Cycle 17: After refmac, R = 0.2486 (Rfree = 0.000) for 4338 atoms. Found 10 (32 requested) and removed 28 (16 requested) atoms. Cycle 18: After refmac, R = 0.2464 (Rfree = 0.000) for 4312 atoms. Found 8 (32 requested) and removed 25 (16 requested) atoms. Cycle 19: After refmac, R = 0.2438 (Rfree = 0.000) for 4283 atoms. Found 14 (32 requested) and removed 19 (16 requested) atoms. Cycle 20: After refmac, R = 0.2371 (Rfree = 0.000) for 4277 atoms. Found 6 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 4447 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4467 seeds are put forward Round 1: 284 peptides, 43 chains. Longest chain 14 peptides. Score 0.462 Round 2: 314 peptides, 41 chains. Longest chain 17 peptides. Score 0.544 Round 3: 309 peptides, 41 chains. Longest chain 17 peptides. Score 0.534 Round 4: 305 peptides, 41 chains. Longest chain 15 peptides. Score 0.526 Round 5: 312 peptides, 40 chains. Longest chain 26 peptides. Score 0.549 Taking the results from Round 5 Chains 43, Residues 272, Estimated correctness of the model 11.2 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9821 restraints for refining 4365 atoms. 8695 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2684 (Rfree = 0.000) for 4365 atoms. Found 27 (32 requested) and removed 26 (16 requested) atoms. Cycle 22: After refmac, R = 0.2576 (Rfree = 0.000) for 4354 atoms. Found 18 (32 requested) and removed 26 (16 requested) atoms. Cycle 23: After refmac, R = 0.2445 (Rfree = 0.000) for 4335 atoms. Found 11 (32 requested) and removed 21 (16 requested) atoms. Cycle 24: After refmac, R = 0.2347 (Rfree = 0.000) for 4314 atoms. Found 10 (32 requested) and removed 18 (16 requested) atoms. Cycle 25: After refmac, R = 0.2329 (Rfree = 0.000) for 4303 atoms. Found 5 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 4461 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4479 seeds are put forward Round 1: 269 peptides, 46 chains. Longest chain 14 peptides. Score 0.397 Round 2: 297 peptides, 45 chains. Longest chain 16 peptides. Score 0.471 Round 3: 310 peptides, 46 chains. Longest chain 21 peptides. Score 0.490 Round 4: 299 peptides, 40 chains. Longest chain 17 peptides. Score 0.523 Round 5: 298 peptides, 44 chains. Longest chain 24 peptides. Score 0.483 Taking the results from Round 4 Chains 40, Residues 259, Estimated correctness of the model 1.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 10252 restraints for refining 4364 atoms. 9256 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2526 (Rfree = 0.000) for 4364 atoms. Found 27 (32 requested) and removed 22 (16 requested) atoms. Cycle 27: After refmac, R = 0.2478 (Rfree = 0.000) for 4351 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 28: After refmac, R = 0.2416 (Rfree = 0.000) for 4345 atoms. Found 31 (32 requested) and removed 26 (16 requested) atoms. Cycle 29: After refmac, R = 0.2316 (Rfree = 0.000) for 4340 atoms. Found 17 (32 requested) and removed 23 (16 requested) atoms. Cycle 30: After refmac, R = 0.2260 (Rfree = 0.000) for 4324 atoms. Found 20 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.34 Search for helices and strands: 0 residues in 0 chains, 4487 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 4504 seeds are put forward Round 1: 256 peptides, 42 chains. Longest chain 12 peptides. Score 0.407 Round 2: 303 peptides, 45 chains. Longest chain 14 peptides. Score 0.484 Round 3: 290 peptides, 42 chains. Longest chain 23 peptides. Score 0.485 Round 4: 287 peptides, 42 chains. Longest chain 13 peptides. Score 0.478 Round 5: 307 peptides, 45 chains. Longest chain 13 peptides. Score 0.493 Taking the results from Round 5 Chains 45, Residues 262, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 10215 restraints for refining 4365 atoms. 9212 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2437 (Rfree = 0.000) for 4365 atoms. Found 31 (32 requested) and removed 31 (16 requested) atoms. Cycle 32: After refmac, R = 0.2274 (Rfree = 0.000) for 4345 atoms. Found 12 (32 requested) and removed 21 (16 requested) atoms. Cycle 33: After refmac, R = 0.2232 (Rfree = 0.000) for 4327 atoms. Found 15 (32 requested) and removed 26 (16 requested) atoms. Cycle 34: After refmac, R = 0.2181 (Rfree = 0.000) for 4311 atoms. Found 8 (32 requested) and removed 20 (16 requested) atoms. Cycle 35: After refmac, R = 0.2117 (Rfree = 0.000) for 4295 atoms. Found 12 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 4477 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4490 seeds are put forward Round 1: 241 peptides, 44 chains. Longest chain 11 peptides. Score 0.349 Round 2: 272 peptides, 40 chains. Longest chain 13 peptides. Score 0.465 Round 3: 280 peptides, 37 chains. Longest chain 14 peptides. Score 0.512 Round 4: 274 peptides, 37 chains. Longest chain 18 peptides. Score 0.499 Round 5: 275 peptides, 36 chains. Longest chain 21 peptides. Score 0.511 Taking the results from Round 3 Chains 38, Residues 243, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9977 restraints for refining 4365 atoms. 8979 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2296 (Rfree = 0.000) for 4365 atoms. Found 22 (32 requested) and removed 24 (16 requested) atoms. Cycle 37: After refmac, R = 0.2259 (Rfree = 0.000) for 4357 atoms. Found 15 (32 requested) and removed 23 (16 requested) atoms. Cycle 38: After refmac, R = 0.2145 (Rfree = 0.000) for 4339 atoms. Found 14 (32 requested) and removed 22 (16 requested) atoms. Cycle 39: After refmac, R = 0.2146 (Rfree = 0.000) for 4325 atoms. Found 19 (32 requested) and removed 19 (16 requested) atoms. Cycle 40: After refmac, R = 0.2076 (Rfree = 0.000) for 4319 atoms. Found 13 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 4482 seeds are put forward NCS extension: 9 residues added (4 deleted due to clashes), 4491 seeds are put forward Round 1: 227 peptides, 40 chains. Longest chain 11 peptides. Score 0.357 Round 2: 239 peptides, 36 chains. Longest chain 14 peptides. Score 0.430 Round 3: 253 peptides, 39 chains. Longest chain 13 peptides. Score 0.431 Round 4: 262 peptides, 37 chains. Longest chain 17 peptides. Score 0.472 Round 5: 261 peptides, 37 chains. Longest chain 19 peptides. Score 0.470 Taking the results from Round 4 Chains 37, Residues 225, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 10235 restraints for refining 4364 atoms. 9372 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2419 (Rfree = 0.000) for 4364 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 42: After refmac, R = 0.2343 (Rfree = 0.000) for 4360 atoms. Found 27 (32 requested) and removed 22 (16 requested) atoms. Cycle 43: After refmac, R = 0.2263 (Rfree = 0.000) for 4355 atoms. Found 22 (32 requested) and removed 20 (16 requested) atoms. Cycle 44: After refmac, R = 0.2218 (Rfree = 0.000) for 4349 atoms. Found 11 (32 requested) and removed 24 (16 requested) atoms. Cycle 45: After refmac, R = 0.2202 (Rfree = 0.000) for 4333 atoms. Found 13 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 4513 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 4535 seeds are put forward Round 1: 224 peptides, 43 chains. Longest chain 10 peptides. Score 0.315 Round 2: 253 peptides, 40 chains. Longest chain 15 peptides. Score 0.421 Round 3: 251 peptides, 41 chains. Longest chain 12 peptides. Score 0.406 Round 4: 254 peptides, 43 chains. Longest chain 12 peptides. Score 0.392 Round 5: 274 peptides, 43 chains. Longest chain 14 peptides. Score 0.439 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 231, 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 2ffj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9629 reflections ( 99.03 % complete ) and 10183 restraints for refining 4365 atoms. 9302 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2450 (Rfree = 0.000) for 4365 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2452 (Rfree = 0.000) for 4333 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2425 (Rfree = 0.000) for 4305 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2427 (Rfree = 0.000) for 4285 atoms. TimeTaking 49.18