Sun 23 Dec 23:52:58 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-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 23:53:03 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-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 430 and 0 Target number of residues in the AU: 430 Target solvent content: 0.6531 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 80.03 8146 reflections ( 98.92 % complete ) and 0 restraints for refining 5290 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3320 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3271 (Rfree = 0.000) for 5290 atoms. Found 33 (33 requested) and removed 43 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 5399 seeds are put forward NCS extension: 0 residues added, 5399 seeds are put forward Round 1: 272 peptides, 49 chains. Longest chain 15 peptides. Score 0.373 Round 2: 336 peptides, 45 chains. Longest chain 19 peptides. Score 0.552 Round 3: 354 peptides, 42 chains. Longest chain 19 peptides. Score 0.610 Round 4: 359 peptides, 37 chains. Longest chain 23 peptides. Score 0.657 Round 5: 359 peptides, 36 chains. Longest chain 24 peptides. Score 0.665 Taking the results from Round 5 Chains 38, Residues 323, Estimated correctness of the model 38.3 % 3 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9169 restraints for refining 4349 atoms. 7712 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2770 (Rfree = 0.000) for 4349 atoms. Found 13 (27 requested) and removed 64 (13 requested) atoms. Cycle 2: After refmac, R = 0.2627 (Rfree = 0.000) for 4193 atoms. Found 15 (27 requested) and removed 40 (13 requested) atoms. Cycle 3: After refmac, R = 0.2531 (Rfree = 0.000) for 4123 atoms. Found 15 (26 requested) and removed 23 (13 requested) atoms. Cycle 4: After refmac, R = 0.2470 (Rfree = 0.000) for 4086 atoms. Found 8 (26 requested) and removed 30 (13 requested) atoms. Cycle 5: After refmac, R = 0.2442 (Rfree = 0.000) for 4051 atoms. Found 8 (26 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 4233 seeds are put forward NCS extension: 12 residues added (7 deleted due to clashes), 4245 seeds are put forward Round 1: 326 peptides, 48 chains. Longest chain 19 peptides. Score 0.505 Round 2: 344 peptides, 45 chains. Longest chain 24 peptides. Score 0.567 Round 3: 353 peptides, 43 chains. Longest chain 22 peptides. Score 0.601 Round 4: 336 peptides, 44 chains. Longest chain 19 peptides. Score 0.561 Round 5: 332 peptides, 44 chains. Longest chain 25 peptides. Score 0.553 Taking the results from Round 3 Chains 43, Residues 310, Estimated correctness of the model 15.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9089 restraints for refining 4105 atoms. 7892 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2799 (Rfree = 0.000) for 4105 atoms. Found 24 (26 requested) and removed 48 (13 requested) atoms. Cycle 7: After refmac, R = 0.2658 (Rfree = 0.000) for 4042 atoms. Found 23 (26 requested) and removed 38 (13 requested) atoms. Cycle 8: After refmac, R = 0.2470 (Rfree = 0.000) for 4005 atoms. Found 14 (25 requested) and removed 28 (12 requested) atoms. Cycle 9: After refmac, R = 0.2384 (Rfree = 0.000) for 3981 atoms. Found 21 (25 requested) and removed 19 (12 requested) atoms. Cycle 10: After refmac, R = 0.2320 (Rfree = 0.000) for 3973 atoms. Found 15 (25 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 4198 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 4216 seeds are put forward Round 1: 291 peptides, 51 chains. Longest chain 13 peptides. Score 0.398 Round 2: 320 peptides, 45 chains. Longest chain 18 peptides. Score 0.520 Round 3: 339 peptides, 47 chains. Longest chain 20 peptides. Score 0.541 Round 4: 341 peptides, 43 chains. Longest chain 19 peptides. Score 0.579 Round 5: 351 peptides, 43 chains. Longest chain 20 peptides. Score 0.597 Taking the results from Round 5 Chains 45, Residues 308, Estimated correctness of the model 13.5 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9116 restraints for refining 4195 atoms. 7843 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2666 (Rfree = 0.000) for 4195 atoms. Found 15 (26 requested) and removed 48 (13 requested) atoms. Cycle 12: After refmac, R = 0.2573 (Rfree = 0.000) for 4136 atoms. Found 11 (26 requested) and removed 27 (13 requested) atoms. Cycle 13: After refmac, R = 0.2531 (Rfree = 0.000) for 4110 atoms. Found 7 (26 requested) and removed 28 (13 requested) atoms. Cycle 14: After refmac, R = 0.2457 (Rfree = 0.000) for 4079 atoms. Found 7 (26 requested) and removed 18 (13 requested) atoms. Cycle 15: After refmac, R = 0.2481 (Rfree = 0.000) for 4065 atoms. Found 2 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 4206 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 4222 seeds are put forward Round 1: 303 peptides, 49 chains. Longest chain 13 peptides. Score 0.446 Round 2: 334 peptides, 40 chains. Longest chain 25 peptides. Score 0.591 Round 3: 334 peptides, 43 chains. Longest chain 16 peptides. Score 0.566 Round 4: 332 peptides, 45 chains. Longest chain 17 peptides. Score 0.544 Round 5: 347 peptides, 43 chains. Longest chain 23 peptides. Score 0.590 Taking the results from Round 2 Chains 41, Residues 294, Estimated correctness of the model 11.1 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9161 restraints for refining 4191 atoms. 7994 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2630 (Rfree = 0.000) for 4191 atoms. Found 24 (26 requested) and removed 34 (13 requested) atoms. Cycle 17: After refmac, R = 0.2545 (Rfree = 0.000) for 4167 atoms. Found 20 (26 requested) and removed 28 (13 requested) atoms. Cycle 18: After refmac, R = 0.2332 (Rfree = 0.000) for 4156 atoms. Found 6 (26 requested) and removed 18 (13 requested) atoms. Cycle 19: After refmac, R = 0.2355 (Rfree = 0.000) for 4134 atoms. Found 10 (26 requested) and removed 19 (13 requested) atoms. Cycle 20: After refmac, R = 0.2361 (Rfree = 0.000) for 4123 atoms. Found 6 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 4276 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 4297 seeds are put forward Round 1: 277 peptides, 43 chains. Longest chain 14 peptides. Score 0.446 Round 2: 326 peptides, 46 chains. Longest chain 18 peptides. Score 0.523 Round 3: 326 peptides, 45 chains. Longest chain 20 peptides. Score 0.532 Round 4: 318 peptides, 42 chains. Longest chain 18 peptides. Score 0.543 Round 5: 334 peptides, 46 chains. Longest chain 17 peptides. Score 0.539 Taking the results from Round 4 Chains 42, Residues 276, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9663 restraints for refining 4268 atoms. 8601 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2673 (Rfree = 0.000) for 4268 atoms. Found 21 (27 requested) and removed 43 (13 requested) atoms. Cycle 22: After refmac, R = 0.2455 (Rfree = 0.000) for 4231 atoms. Found 21 (27 requested) and removed 25 (13 requested) atoms. Cycle 23: After refmac, R = 0.2482 (Rfree = 0.000) for 4217 atoms. Found 13 (27 requested) and removed 29 (13 requested) atoms. Cycle 24: After refmac, R = 0.2329 (Rfree = 0.000) for 4198 atoms. Found 5 (26 requested) and removed 20 (13 requested) atoms. Cycle 25: After refmac, R = 0.2412 (Rfree = 0.000) for 4179 atoms. Found 13 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 4353 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 4364 seeds are put forward Round 1: 262 peptides, 47 chains. Longest chain 14 peptides. Score 0.369 Round 2: 283 peptides, 46 chains. Longest chain 12 peptides. Score 0.430 Round 3: 329 peptides, 51 chains. Longest chain 18 peptides. Score 0.484 Round 4: 327 peptides, 47 chains. Longest chain 19 peptides. Score 0.516 Round 5: 315 peptides, 47 chains. Longest chain 16 peptides. Score 0.491 Taking the results from Round 4 Chains 47, Residues 280, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9803 restraints for refining 4349 atoms. 8652 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2600 (Rfree = 0.000) for 4349 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 27: After refmac, R = 0.2429 (Rfree = 0.000) for 4324 atoms. Found 9 (27 requested) and removed 22 (13 requested) atoms. Cycle 28: After refmac, R = 0.2341 (Rfree = 0.000) for 4301 atoms. Found 14 (27 requested) and removed 22 (13 requested) atoms. Cycle 29: After refmac, R = 0.2291 (Rfree = 0.000) for 4280 atoms. Found 10 (27 requested) and removed 20 (13 requested) atoms. Cycle 30: After refmac, R = 0.2243 (Rfree = 0.000) for 4256 atoms. Found 11 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 4402 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 4419 seeds are put forward Round 1: 244 peptides, 42 chains. Longest chain 15 peptides. Score 0.378 Round 2: 286 peptides, 46 chains. Longest chain 14 peptides. Score 0.437 Round 3: 296 peptides, 46 chains. Longest chain 15 peptides. Score 0.459 Round 4: 320 peptides, 46 chains. Longest chain 19 peptides. Score 0.511 Round 5: 316 peptides, 47 chains. Longest chain 19 peptides. Score 0.493 Taking the results from Round 4 Chains 49, Residues 274, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9850 restraints for refining 4349 atoms. 8710 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2598 (Rfree = 0.000) for 4349 atoms. Found 26 (27 requested) and removed 28 (13 requested) atoms. Cycle 32: After refmac, R = 0.2384 (Rfree = 0.000) for 4319 atoms. Found 9 (27 requested) and removed 21 (13 requested) atoms. Cycle 33: After refmac, R = 0.2347 (Rfree = 0.000) for 4298 atoms. Found 13 (27 requested) and removed 17 (13 requested) atoms. Cycle 34: After refmac, R = 0.2335 (Rfree = 0.000) for 4285 atoms. Found 12 (27 requested) and removed 24 (13 requested) atoms. Cycle 35: After refmac, R = 0.2175 (Rfree = 0.000) for 4266 atoms. Found 6 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 4406 seeds are put forward NCS extension: 8 residues added (5 deleted due to clashes), 4414 seeds are put forward Round 1: 245 peptides, 48 chains. Longest chain 15 peptides. Score 0.315 Round 2: 278 peptides, 44 chains. Longest chain 19 peptides. Score 0.438 Round 3: 291 peptides, 41 chains. Longest chain 25 peptides. Score 0.497 Round 4: 288 peptides, 42 chains. Longest chain 23 peptides. Score 0.481 Round 5: 280 peptides, 44 chains. Longest chain 14 peptides. Score 0.443 Taking the results from Round 3 Chains 45, Residues 250, Estimated correctness of the model 0.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9590 restraints for refining 4351 atoms. 8477 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2441 (Rfree = 0.000) for 4351 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 37: After refmac, R = 0.2414 (Rfree = 0.000) for 4329 atoms. Found 21 (27 requested) and removed 34 (13 requested) atoms. Cycle 38: After refmac, R = 0.2322 (Rfree = 0.000) for 4292 atoms. Found 15 (27 requested) and removed 28 (13 requested) atoms. Cycle 39: After refmac, R = 0.2294 (Rfree = 0.000) for 4265 atoms. Found 7 (27 requested) and removed 20 (13 requested) atoms. Cycle 40: After refmac, R = 0.2229 (Rfree = 0.000) for 4245 atoms. Found 12 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 4381 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 4406 seeds are put forward Round 1: 243 peptides, 47 chains. Longest chain 11 peptides. Score 0.321 Round 2: 280 peptides, 46 chains. Longest chain 15 peptides. Score 0.423 Round 3: 280 peptides, 44 chains. Longest chain 27 peptides. Score 0.443 Round 4: 293 peptides, 45 chains. Longest chain 20 peptides. Score 0.462 Round 5: 276 peptides, 44 chains. Longest chain 21 peptides. Score 0.434 Taking the results from Round 4 Chains 47, Residues 248, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9330 restraints for refining 4288 atoms. 8230 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2555 (Rfree = 0.000) for 4288 atoms. Found 21 (27 requested) and removed 45 (13 requested) atoms. Cycle 42: After refmac, R = 0.2350 (Rfree = 0.000) for 4254 atoms. Found 12 (27 requested) and removed 21 (13 requested) atoms. Cycle 43: After refmac, R = 0.2307 (Rfree = 0.000) for 4239 atoms. Found 8 (27 requested) and removed 20 (13 requested) atoms. Cycle 44: After refmac, R = 0.2251 (Rfree = 0.000) for 4220 atoms. Found 10 (27 requested) and removed 20 (13 requested) atoms. Cycle 45: After refmac, R = 0.2203 (Rfree = 0.000) for 4203 atoms. Found 10 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 4344 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 4370 seeds are put forward Round 1: 216 peptides, 43 chains. Longest chain 9 peptides. Score 0.294 Round 2: 245 peptides, 42 chains. Longest chain 19 peptides. Score 0.380 Round 3: 242 peptides, 38 chains. Longest chain 14 peptides. Score 0.416 Round 4: 243 peptides, 41 chains. Longest chain 14 peptides. Score 0.386 Round 5: 242 peptides, 40 chains. Longest chain 13 peptides. Score 0.394 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 204, 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. 8146 reflections ( 98.92 % complete ) and 10066 restraints for refining 4265 atoms. 9288 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2541 (Rfree = 0.000) for 4265 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2386 (Rfree = 0.000) for 4239 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2346 (Rfree = 0.000) for 4221 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2253 (Rfree = 0.000) for 4205 atoms. TimeTaking 53.45