Mon 24 Dec 07:41:21 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 2ffj-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.8-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/2ffj-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.8-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 07:41:25 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/2ffj-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.8-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 417 and 0 Target number of residues in the AU: 417 Target solvent content: 0.6636 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-3.8-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: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-3.8-parrot-noncs.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 3.800 Wilson plot Bfac: 87.62 6939 reflections ( 98.80 % complete ) and 0 restraints for refining 5327 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3461 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3586 (Rfree = 0.000) for 5327 atoms. Found 29 (29 requested) and removed 49 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 5467 seeds are put forward NCS extension: 0 residues added, 5467 seeds are put forward Round 1: 203 peptides, 42 chains. Longest chain 9 peptides. Score 0.270 Round 2: 269 peptides, 43 chains. Longest chain 20 peptides. Score 0.428 Round 3: 306 peptides, 45 chains. Longest chain 18 peptides. Score 0.491 Round 4: 310 peptides, 45 chains. Longest chain 26 peptides. Score 0.499 Round 5: 300 peptides, 39 chains. Longest chain 18 peptides. Score 0.534 Taking the results from Round 5 Chains 40, Residues 261, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 10328 restraints for refining 4340 atoms. 9292 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2832 (Rfree = 0.000) for 4340 atoms. Found 23 (23 requested) and removed 60 (11 requested) atoms. Cycle 2: After refmac, R = 0.2556 (Rfree = 0.000) for 4217 atoms. Found 21 (23 requested) and removed 39 (11 requested) atoms. Cycle 3: After refmac, R = 0.2686 (Rfree = 0.000) for 4152 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 4: After refmac, R = 0.2520 (Rfree = 0.000) for 4114 atoms. Found 22 (22 requested) and removed 39 (11 requested) atoms. Cycle 5: After refmac, R = 0.2443 (Rfree = 0.000) for 4073 atoms. Found 21 (22 requested) and removed 30 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 4282 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 4297 seeds are put forward Round 1: 231 peptides, 40 chains. Longest chain 14 peptides. Score 0.367 Round 2: 259 peptides, 39 chains. Longest chain 20 peptides. Score 0.445 Round 3: 264 peptides, 39 chains. Longest chain 17 peptides. Score 0.457 Round 4: 266 peptides, 39 chains. Longest chain 15 peptides. Score 0.461 Round 5: 262 peptides, 38 chains. Longest chain 20 peptides. Score 0.462 Taking the results from Round 5 Chains 38, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9656 restraints for refining 4080 atoms. 8798 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2738 (Rfree = 0.000) for 4080 atoms. Found 13 (22 requested) and removed 51 (11 requested) atoms. Cycle 7: After refmac, R = 0.2605 (Rfree = 0.000) for 4008 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 8: After refmac, R = 0.2384 (Rfree = 0.000) for 3974 atoms. Found 20 (21 requested) and removed 28 (10 requested) atoms. Cycle 9: After refmac, R = 0.2392 (Rfree = 0.000) for 3943 atoms. Found 18 (21 requested) and removed 26 (10 requested) atoms. Cycle 10: After refmac, R = 0.2482 (Rfree = 0.000) for 3919 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 4144 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4164 seeds are put forward Round 1: 248 peptides, 47 chains. Longest chain 12 peptides. Score 0.334 Round 2: 295 peptides, 41 chains. Longest chain 21 peptides. Score 0.505 Round 3: 299 peptides, 44 chains. Longest chain 14 peptides. Score 0.485 Round 4: 300 peptides, 43 chains. Longest chain 17 peptides. Score 0.497 Round 5: 314 peptides, 45 chains. Longest chain 15 peptides. Score 0.508 Taking the results from Round 5 Chains 45, Residues 269, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9588 restraints for refining 4174 atoms. 8557 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2821 (Rfree = 0.000) for 4174 atoms. Found 22 (22 requested) and removed 60 (11 requested) atoms. Cycle 12: After refmac, R = 0.2470 (Rfree = 0.000) for 4097 atoms. Found 20 (22 requested) and removed 41 (11 requested) atoms. Cycle 13: After refmac, R = 0.2287 (Rfree = 0.000) for 4055 atoms. Found 15 (22 requested) and removed 34 (11 requested) atoms. Cycle 14: After refmac, R = 0.2036 (Rfree = 0.000) for 4022 atoms. Found 4 (22 requested) and removed 23 (11 requested) atoms. Cycle 15: After refmac, R = 0.2241 (Rfree = 0.000) for 3993 atoms. Found 11 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 4227 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4247 seeds are put forward Round 1: 259 peptides, 47 chains. Longest chain 11 peptides. Score 0.361 Round 2: 273 peptides, 41 chains. Longest chain 17 peptides. Score 0.457 Round 3: 267 peptides, 39 chains. Longest chain 17 peptides. Score 0.464 Round 4: 275 peptides, 41 chains. Longest chain 14 peptides. Score 0.462 Round 5: 264 peptides, 39 chains. Longest chain 16 peptides. Score 0.457 Taking the results from Round 3 Chains 39, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9885 restraints for refining 4212 atoms. 9012 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2466 (Rfree = 0.000) for 4212 atoms. Found 10 (23 requested) and removed 38 (11 requested) atoms. Cycle 17: After refmac, R = 0.2571 (Rfree = 0.000) for 4162 atoms. Found 23 (23 requested) and removed 38 (11 requested) atoms. Cycle 18: After refmac, R = 0.2431 (Rfree = 0.000) for 4133 atoms. Found 14 (22 requested) and removed 25 (11 requested) atoms. Cycle 19: After refmac, R = 0.2634 (Rfree = 0.000) for 4109 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 20: After refmac, R = 0.2420 (Rfree = 0.000) for 4083 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 4280 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4298 seeds are put forward Round 1: 239 peptides, 44 chains. Longest chain 11 peptides. Score 0.343 Round 2: 263 peptides, 42 chains. Longest chain 13 peptides. Score 0.424 Round 3: 276 peptides, 42 chains. Longest chain 12 peptides. Score 0.454 Round 4: 286 peptides, 44 chains. Longest chain 13 peptides. Score 0.456 Round 5: 303 peptides, 44 chains. Longest chain 15 peptides. Score 0.494 Taking the results from Round 5 Chains 44, Residues 259, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9478 restraints for refining 4172 atoms. 8486 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2639 (Rfree = 0.000) for 4172 atoms. Found 22 (22 requested) and removed 41 (11 requested) atoms. Cycle 22: After refmac, R = 0.2376 (Rfree = 0.000) for 4117 atoms. Found 19 (22 requested) and removed 29 (11 requested) atoms. Cycle 23: After refmac, R = 0.2320 (Rfree = 0.000) for 4081 atoms. Found 13 (22 requested) and removed 15 (11 requested) atoms. Cycle 24: After refmac, R = 0.2482 (Rfree = 0.000) for 4064 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 25: After refmac, R = 0.2313 (Rfree = 0.000) for 4046 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 4261 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4278 seeds are put forward Round 1: 227 peptides, 43 chains. Longest chain 12 peptides. Score 0.323 Round 2: 259 peptides, 42 chains. Longest chain 16 peptides. Score 0.414 Round 3: 262 peptides, 42 chains. Longest chain 14 peptides. Score 0.421 Round 4: 253 peptides, 38 chains. Longest chain 14 peptides. Score 0.442 Round 5: 267 peptides, 39 chains. Longest chain 13 peptides. Score 0.464 Taking the results from Round 5 Chains 39, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9985 restraints for refining 4255 atoms. 9112 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2581 (Rfree = 0.000) for 4255 atoms. Found 13 (23 requested) and removed 35 (11 requested) atoms. Cycle 27: After refmac, R = 0.2316 (Rfree = 0.000) for 4201 atoms. Found 11 (23 requested) and removed 24 (11 requested) atoms. Cycle 28: After refmac, R = 0.2280 (Rfree = 0.000) for 4150 atoms. Found 9 (23 requested) and removed 23 (11 requested) atoms. Cycle 29: After refmac, R = 0.1888 (Rfree = 0.000) for 4117 atoms. Found 3 (22 requested) and removed 19 (11 requested) atoms. Cycle 30: After refmac, R = 0.1850 (Rfree = 0.000) for 4089 atoms. Found 4 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 4267 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4283 seeds are put forward Round 1: 190 peptides, 39 chains. Longest chain 9 peptides. Score 0.269 Round 2: 234 peptides, 42 chains. Longest chain 11 peptides. Score 0.353 Round 3: 242 peptides, 41 chains. Longest chain 13 peptides. Score 0.384 Round 4: 242 peptides, 40 chains. Longest chain 13 peptides. Score 0.394 Round 5: 244 peptides, 36 chains. Longest chain 14 peptides. Score 0.442 Taking the results from Round 5 Chains 36, Residues 208, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9786 restraints for refining 4230 atoms. 8961 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2715 (Rfree = 0.000) for 4230 atoms. Found 23 (23 requested) and removed 44 (11 requested) atoms. Cycle 32: After refmac, R = 0.2387 (Rfree = 0.000) for 4187 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 33: After refmac, R = 0.2266 (Rfree = 0.000) for 4150 atoms. Found 21 (22 requested) and removed 29 (11 requested) atoms. Cycle 34: After refmac, R = 0.2117 (Rfree = 0.000) for 4125 atoms. Found 16 (22 requested) and removed 23 (11 requested) atoms. Cycle 35: After refmac, R = 0.2142 (Rfree = 0.000) for 4108 atoms. Found 17 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 4243 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4258 seeds are put forward Round 1: 207 peptides, 42 chains. Longest chain 10 peptides. Score 0.281 Round 2: 236 peptides, 39 chains. Longest chain 14 peptides. Score 0.390 Round 3: 238 peptides, 39 chains. Longest chain 12 peptides. Score 0.395 Round 4: 252 peptides, 38 chains. Longest chain 13 peptides. Score 0.439 Round 5: 261 peptides, 41 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 4 Chains 38, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9652 restraints for refining 4251 atoms. 8834 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2486 (Rfree = 0.000) for 4251 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 37: After refmac, R = 0.2369 (Rfree = 0.000) for 4199 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 38: After refmac, R = 0.2118 (Rfree = 0.000) for 4174 atoms. Found 13 (23 requested) and removed 24 (11 requested) atoms. Cycle 39: After refmac, R = 0.2202 (Rfree = 0.000) for 4153 atoms. Found 19 (22 requested) and removed 27 (11 requested) atoms. Cycle 40: After refmac, R = 0.2306 (Rfree = 0.000) for 4138 atoms. Found 18 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 4334 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4350 seeds are put forward Round 1: 193 peptides, 41 chains. Longest chain 12 peptides. Score 0.254 Round 2: 206 peptides, 38 chains. Longest chain 11 peptides. Score 0.325 Round 3: 199 peptides, 38 chains. Longest chain 10 peptides. Score 0.306 Round 4: 210 peptides, 37 chains. Longest chain 13 peptides. Score 0.347 Round 5: 221 peptides, 40 chains. Longest chain 12 peptides. Score 0.341 Taking the results from Round 4 Chains 37, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9498 restraints for refining 4091 atoms. 8843 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2479 (Rfree = 0.000) for 4091 atoms. Found 17 (22 requested) and removed 44 (11 requested) atoms. Cycle 42: After refmac, R = 0.2456 (Rfree = 0.000) for 4044 atoms. Found 17 (22 requested) and removed 37 (11 requested) atoms. Cycle 43: After refmac, R = 0.2293 (Rfree = 0.000) for 4011 atoms. Found 20 (22 requested) and removed 23 (11 requested) atoms. Cycle 44: After refmac, R = 0.2273 (Rfree = 0.000) for 3994 atoms. Found 19 (22 requested) and removed 19 (11 requested) atoms. Cycle 45: After refmac, R = 0.2375 (Rfree = 0.000) for 3989 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 4155 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4171 seeds are put forward Round 1: 144 peptides, 27 chains. Longest chain 12 peptides. Score 0.285 Round 2: 178 peptides, 30 chains. Longest chain 13 peptides. Score 0.343 Round 3: 176 peptides, 30 chains. Longest chain 12 peptides. Score 0.338 Round 4: 176 peptides, 31 chains. Longest chain 12 peptides. Score 0.326 Round 5: 174 peptides, 31 chains. Longest chain 10 peptides. Score 0.321 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 148, 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. 6939 reflections ( 98.80 % complete ) and 9301 restraints for refining 3990 atoms. 8739 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2581 (Rfree = 0.000) for 3990 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2380 (Rfree = 0.000) for 3962 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2420 (Rfree = 0.000) for 3938 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2390 (Rfree = 0.000) for 3916 atoms. TimeTaking 43.37