null Sun 23 Dec 22:22:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ffj-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-parrot-hancs ############### 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 22:23:03 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/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-parrot-hancs/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-hancs.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-hancs.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 5336 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3339 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3447 (Rfree = 0.000) for 5336 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 5455 seeds are put forward NCS extension: 0 residues added, 5455 seeds are put forward Round 1: 265 peptides, 43 chains. Longest chain 14 peptides. Score 0.418 Round 2: 327 peptides, 44 chains. Longest chain 19 peptides. Score 0.543 Round 3: 335 peptides, 39 chains. Longest chain 22 peptides. Score 0.601 Round 4: 345 peptides, 42 chains. Longest chain 21 peptides. Score 0.594 Round 5: 362 peptides, 36 chains. Longest chain 28 peptides. Score 0.669 Taking the results from Round 5 Chains 42, Residues 326, Estimated correctness of the model 39.6 % 5 chains (65 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9013 restraints for refining 4349 atoms. 7491 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2849 (Rfree = 0.000) for 4349 atoms. Found 22 (27 requested) and removed 39 (13 requested) atoms. Cycle 2: After refmac, R = 0.2802 (Rfree = 0.000) for 4214 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 3: After refmac, R = 0.2676 (Rfree = 0.000) for 4145 atoms. Found 19 (26 requested) and removed 33 (13 requested) atoms. Cycle 4: After refmac, R = 0.2608 (Rfree = 0.000) for 4081 atoms. Found 19 (26 requested) and removed 31 (13 requested) atoms. Cycle 5: After refmac, R = 0.2603 (Rfree = 0.000) for 4041 atoms. Found 21 (26 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 4191 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 4212 seeds are put forward Round 1: 302 peptides, 46 chains. Longest chain 18 peptides. Score 0.473 Round 2: 335 peptides, 42 chains. Longest chain 25 peptides. Score 0.576 Round 3: 346 peptides, 41 chains. Longest chain 27 peptides. Score 0.604 Round 4: 345 peptides, 42 chains. Longest chain 26 peptides. Score 0.594 Round 5: 341 peptides, 42 chains. Longest chain 27 peptides. Score 0.587 Taking the results from Round 3 Chains 44, Residues 305, Estimated correctness of the model 16.2 % 5 chains (73 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 8610 restraints for refining 4192 atoms. 7187 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2723 (Rfree = 0.000) for 4192 atoms. Found 26 (26 requested) and removed 63 (13 requested) atoms. Cycle 7: After refmac, R = 0.2565 (Rfree = 0.000) for 4099 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. Cycle 8: After refmac, R = 0.2447 (Rfree = 0.000) for 4071 atoms. Found 18 (26 requested) and removed 27 (13 requested) atoms. Cycle 9: After refmac, R = 0.2196 (Rfree = 0.000) for 4035 atoms. Found 10 (26 requested) and removed 20 (13 requested) atoms. Cycle 10: After refmac, R = 0.2127 (Rfree = 0.000) for 4012 atoms. Found 7 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 4171 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4183 seeds are put forward Round 1: 301 peptides, 51 chains. Longest chain 16 peptides. Score 0.421 Round 2: 324 peptides, 45 chains. Longest chain 19 peptides. Score 0.528 Round 3: 343 peptides, 46 chains. Longest chain 20 peptides. Score 0.557 Round 4: 343 peptides, 43 chains. Longest chain 19 peptides. Score 0.583 Round 5: 356 peptides, 47 chains. Longest chain 16 peptides. Score 0.573 Taking the results from Round 4 Chains 45, Residues 300, Estimated correctness of the model 7.9 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9140 restraints for refining 4231 atoms. 7849 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2731 (Rfree = 0.000) for 4231 atoms. Found 23 (27 requested) and removed 52 (13 requested) atoms. Cycle 12: After refmac, R = 0.2458 (Rfree = 0.000) for 4171 atoms. Found 10 (26 requested) and removed 32 (13 requested) atoms. Cycle 13: After refmac, R = 0.2373 (Rfree = 0.000) for 4134 atoms. Found 19 (26 requested) and removed 33 (13 requested) atoms. Cycle 14: After refmac, R = 0.2159 (Rfree = 0.000) for 4110 atoms. Found 4 (26 requested) and removed 24 (13 requested) atoms. Cycle 15: After refmac, R = 0.2118 (Rfree = 0.000) for 4084 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.53 Search for helices and strands: 0 residues in 0 chains, 4229 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4243 seeds are put forward Round 1: 308 peptides, 53 chains. Longest chain 15 peptides. Score 0.417 Round 2: 334 peptides, 47 chains. Longest chain 20 peptides. Score 0.531 Round 3: 322 peptides, 44 chains. Longest chain 21 peptides. Score 0.533 Round 4: 324 peptides, 44 chains. Longest chain 19 peptides. Score 0.537 Round 5: 322 peptides, 41 chains. Longest chain 25 peptides. Score 0.560 Taking the results from Round 5 Chains 45, Residues 281, Estimated correctness of the model 0.0 % 3 chains (49 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9449 restraints for refining 4350 atoms. 8187 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2542 (Rfree = 0.000) for 4350 atoms. Found 22 (27 requested) and removed 52 (13 requested) atoms. Cycle 17: After refmac, R = 0.2295 (Rfree = 0.000) for 4295 atoms. Found 12 (27 requested) and removed 28 (13 requested) atoms. Cycle 18: After refmac, R = 0.2301 (Rfree = 0.000) for 4264 atoms. Found 15 (27 requested) and removed 28 (13 requested) atoms. Cycle 19: After refmac, R = 0.2243 (Rfree = 0.000) for 4239 atoms. Found 16 (27 requested) and removed 26 (13 requested) atoms. Cycle 20: After refmac, R = 0.2189 (Rfree = 0.000) for 4220 atoms. Found 15 (27 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 4372 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4392 seeds are put forward Round 1: 266 peptides, 45 chains. Longest chain 22 peptides. Score 0.400 Round 2: 294 peptides, 38 chains. Longest chain 21 peptides. Score 0.531 Round 3: 287 peptides, 37 chains. Longest chain 21 peptides. Score 0.526 Round 4: 293 peptides, 37 chains. Longest chain 21 peptides. Score 0.538 Round 5: 303 peptides, 42 chains. Longest chain 25 peptides. Score 0.513 Taking the results from Round 4 Chains 38, Residues 256, Estimated correctness of the model 0.0 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9762 restraints for refining 4351 atoms. 8643 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2635 (Rfree = 0.000) for 4351 atoms. Found 22 (27 requested) and removed 45 (13 requested) atoms. Cycle 22: After refmac, R = 0.2630 (Rfree = 0.000) for 4307 atoms. Found 25 (27 requested) and removed 35 (13 requested) atoms. Cycle 23: After refmac, R = 0.2359 (Rfree = 0.000) for 4277 atoms. Found 19 (27 requested) and removed 28 (13 requested) atoms. Cycle 24: After refmac, R = 0.2295 (Rfree = 0.000) for 4255 atoms. Found 10 (27 requested) and removed 25 (13 requested) atoms. Cycle 25: After refmac, R = 0.2261 (Rfree = 0.000) for 4230 atoms. Found 14 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 4407 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 4431 seeds are put forward Round 1: 246 peptides, 49 chains. Longest chain 9 peptides. Score 0.306 Round 2: 284 peptides, 48 chains. Longest chain 12 peptides. Score 0.412 Round 3: 281 peptides, 43 chains. Longest chain 13 peptides. Score 0.455 Round 4: 289 peptides, 46 chains. Longest chain 15 peptides. Score 0.444 Round 5: 288 peptides, 44 chains. Longest chain 16 peptides. Score 0.461 Taking the results from Round 5 Chains 45, Residues 244, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9878 restraints for refining 4350 atoms. 8901 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2707 (Rfree = 0.000) for 4350 atoms. Found 23 (27 requested) and removed 34 (13 requested) atoms. Cycle 27: After refmac, R = 0.2456 (Rfree = 0.000) for 4308 atoms. Found 26 (27 requested) and removed 23 (13 requested) atoms. Cycle 28: After refmac, R = 0.2183 (Rfree = 0.000) for 4300 atoms. Found 5 (27 requested) and removed 20 (13 requested) atoms. Cycle 29: After refmac, R = 0.2093 (Rfree = 0.000) for 4274 atoms. Found 4 (27 requested) and removed 19 (13 requested) atoms. Cycle 30: After refmac, R = 0.2035 (Rfree = 0.000) for 4249 atoms. Found 7 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 4398 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 4426 seeds are put forward Round 1: 236 peptides, 46 chains. Longest chain 9 peptides. Score 0.313 Round 2: 272 peptides, 48 chains. Longest chain 13 peptides. Score 0.383 Round 3: 284 peptides, 41 chains. Longest chain 20 peptides. Score 0.482 Round 4: 283 peptides, 42 chains. Longest chain 17 peptides. Score 0.470 Round 5: 298 peptides, 40 chains. Longest chain 20 peptides. Score 0.521 Taking the results from Round 5 Chains 40, Residues 258, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9806 restraints for refining 4351 atoms. 8814 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2524 (Rfree = 0.000) for 4351 atoms. Found 25 (27 requested) and removed 27 (13 requested) atoms. Cycle 32: After refmac, R = 0.2344 (Rfree = 0.000) for 4309 atoms. Found 22 (27 requested) and removed 24 (13 requested) atoms. Cycle 33: After refmac, R = 0.2228 (Rfree = 0.000) for 4282 atoms. Found 15 (27 requested) and removed 18 (13 requested) atoms. Cycle 34: After refmac, R = 0.2102 (Rfree = 0.000) for 4261 atoms. Found 11 (27 requested) and removed 17 (13 requested) atoms. Cycle 35: After refmac, R = 0.2040 (Rfree = 0.000) for 4246 atoms. Found 8 (27 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 4392 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 4419 seeds are put forward Round 1: 228 peptides, 45 chains. Longest chain 12 peptides. Score 0.303 Round 2: 266 peptides, 47 chains. Longest chain 16 peptides. Score 0.379 Round 3: 277 peptides, 45 chains. Longest chain 15 peptides. Score 0.426 Round 4: 285 peptides, 42 chains. Longest chain 21 peptides. Score 0.474 Round 5: 274 peptides, 44 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 4 Chains 42, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9782 restraints for refining 4331 atoms. 8852 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2406 (Rfree = 0.000) for 4331 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 37: After refmac, R = 0.2228 (Rfree = 0.000) for 4314 atoms. Found 17 (27 requested) and removed 23 (13 requested) atoms. Cycle 38: After refmac, R = 0.2140 (Rfree = 0.000) for 4301 atoms. Found 16 (27 requested) and removed 21 (13 requested) atoms. Cycle 39: After refmac, R = 0.1958 (Rfree = 0.000) for 4287 atoms. Found 11 (27 requested) and removed 16 (13 requested) atoms. Cycle 40: After refmac, R = 0.2024 (Rfree = 0.000) for 4280 atoms. Found 14 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 4445 seeds are put forward NCS extension: 39 residues added (0 deleted due to clashes), 4484 seeds are put forward Round 1: 222 peptides, 46 chains. Longest chain 12 peptides. Score 0.276 Round 2: 247 peptides, 45 chains. Longest chain 16 peptides. Score 0.353 Round 3: 242 peptides, 42 chains. Longest chain 13 peptides. Score 0.373 Round 4: 253 peptides, 40 chains. Longest chain 24 peptides. Score 0.421 Round 5: 259 peptides, 43 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 4 Chains 41, Residues 213, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9844 restraints for refining 4351 atoms. 8947 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2281 (Rfree = 0.000) for 4351 atoms. Found 20 (27 requested) and removed 26 (13 requested) atoms. Cycle 42: After refmac, R = 0.2120 (Rfree = 0.000) for 4330 atoms. Found 7 (27 requested) and removed 21 (13 requested) atoms. Cycle 43: After refmac, R = 0.2081 (Rfree = 0.000) for 4310 atoms. Found 6 (27 requested) and removed 16 (13 requested) atoms. Cycle 44: After refmac, R = 0.2077 (Rfree = 0.000) for 4296 atoms. Found 10 (27 requested) and removed 17 (13 requested) atoms. Cycle 45: After refmac, R = 0.1997 (Rfree = 0.000) for 4283 atoms. Found 10 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 4417 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4432 seeds are put forward Round 1: 182 peptides, 37 chains. Longest chain 13 peptides. Score 0.270 Round 2: 223 peptides, 41 chains. Longest chain 11 peptides. Score 0.335 Round 3: 231 peptides, 40 chains. Longest chain 19 peptides. Score 0.367 Round 4: 233 peptides, 42 chains. Longest chain 24 peptides. Score 0.350 Round 5: 237 peptides, 41 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 196, 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 10327 restraints for refining 4351 atoms. 9584 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2322 (Rfree = 0.000) for 4351 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2223 (Rfree = 0.000) for 4331 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2212 (Rfree = 0.000) for 4316 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2142 (Rfree = 0.000) for 4302 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:25:38 GMT 2018 Job finished. TimeTaking 62.76 Used memory is bytes: 18830096