Mon 24 Dec 00:38:52 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 2gfg-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-3.2-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/2gfg-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-3.2-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 00:38:57 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/2gfg-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-3.2-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 429 and 0 Target number of residues in the AU: 429 Target solvent content: 0.6160 Checking the provided sequence file Detected sequence length: 193 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 579 Adjusted target solvent content: 0.48 Input MTZ file: 2gfg-3.2-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: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4632 target number of atoms Had to go as low as 0.65 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: 94.065 3.200 Wilson plot Bfac: 59.54 10582 reflections ( 99.61 % complete ) and 0 restraints for refining 5121 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3575 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3448 (Rfree = 0.000) for 5121 atoms. Found 45 (45 requested) and removed 60 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 5177 seeds are put forward NCS extension: 0 residues added, 5177 seeds are put forward Round 1: 211 peptides, 46 chains. Longest chain 10 peptides. Score 0.252 Round 2: 272 peptides, 49 chains. Longest chain 11 peptides. Score 0.389 Round 3: 296 peptides, 46 chains. Longest chain 14 peptides. Score 0.482 Round 4: 316 peptides, 50 chains. Longest chain 13 peptides. Score 0.488 Round 5: 324 peptides, 50 chains. Longest chain 15 peptides. Score 0.507 Taking the results from Round 5 Chains 50, Residues 274, Estimated correctness of the model 13.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9481 restraints for refining 4229 atoms. 8435 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3017 (Rfree = 0.000) for 4229 atoms. Found 33 (37 requested) and removed 41 (18 requested) atoms. Cycle 2: After refmac, R = 0.2708 (Rfree = 0.000) for 4180 atoms. Found 14 (37 requested) and removed 25 (18 requested) atoms. Cycle 3: After refmac, R = 0.2730 (Rfree = 0.000) for 4142 atoms. Found 22 (37 requested) and removed 23 (18 requested) atoms. Cycle 4: After refmac, R = 0.2508 (Rfree = 0.000) for 4120 atoms. Found 11 (37 requested) and removed 20 (18 requested) atoms. Cycle 5: After refmac, R = 0.2674 (Rfree = 0.000) for 4103 atoms. Found 35 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 4268 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4286 seeds are put forward Round 1: 280 peptides, 50 chains. Longest chain 12 peptides. Score 0.399 Round 2: 304 peptides, 44 chains. Longest chain 16 peptides. Score 0.521 Round 3: 291 peptides, 41 chains. Longest chain 17 peptides. Score 0.522 Round 4: 297 peptides, 45 chains. Longest chain 18 peptides. Score 0.495 Round 5: 284 peptides, 42 chains. Longest chain 18 peptides. Score 0.495 Taking the results from Round 3 Chains 41, Residues 250, Estimated correctness of the model 18.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9553 restraints for refining 4211 atoms. 8594 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2843 (Rfree = 0.000) for 4211 atoms. Found 32 (37 requested) and removed 40 (18 requested) atoms. Cycle 7: After refmac, R = 0.2569 (Rfree = 0.000) for 4181 atoms. Found 22 (37 requested) and removed 36 (18 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2286 (Rfree = 0.000) for 4155 atoms. Found 8 (37 requested) and removed 22 (18 requested) atoms. Cycle 9: After refmac, R = 0.2470 (Rfree = 0.000) for 4131 atoms. Found 21 (37 requested) and removed 22 (18 requested) atoms. Cycle 10: After refmac, R = 0.2421 (Rfree = 0.000) for 4126 atoms. Found 30 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.17 Search for helices and strands: 0 residues in 0 chains, 4270 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4293 seeds are put forward Round 1: 244 peptides, 43 chains. Longest chain 13 peptides. Score 0.383 Round 2: 283 peptides, 44 chains. Longest chain 20 peptides. Score 0.472 Round 3: 295 peptides, 45 chains. Longest chain 13 peptides. Score 0.490 Round 4: 304 peptides, 42 chains. Longest chain 22 peptides. Score 0.541 Round 5: 323 peptides, 49 chains. Longest chain 23 peptides. Score 0.515 Taking the results from Round 4 Chains 42, Residues 262, Estimated correctness of the model 24.2 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9409 restraints for refining 4228 atoms. 8332 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2493 (Rfree = 0.000) for 4228 atoms. Found 19 (37 requested) and removed 36 (18 requested) atoms. Cycle 12: After refmac, R = 0.2291 (Rfree = 0.000) for 4190 atoms. Found 15 (37 requested) and removed 27 (18 requested) atoms. Cycle 13: After refmac, R = 0.2290 (Rfree = 0.000) for 4169 atoms. Found 10 (37 requested) and removed 22 (18 requested) atoms. Cycle 14: After refmac, R = 0.2236 (Rfree = 0.000) for 4147 atoms. Found 20 (37 requested) and removed 28 (18 requested) atoms. Cycle 15: After refmac, R = 0.2037 (Rfree = 0.000) for 4129 atoms. Found 4 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.11 3.19 Search for helices and strands: 0 residues in 0 chains, 4253 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 4275 seeds are put forward Round 1: 260 peptides, 50 chains. Longest chain 14 peptides. Score 0.345 Round 2: 281 peptides, 47 chains. Longest chain 14 peptides. Score 0.435 Round 3: 292 peptides, 44 chains. Longest chain 17 peptides. Score 0.493 Round 4: 287 peptides, 42 chains. Longest chain 18 peptides. Score 0.502 Round 5: 306 peptides, 44 chains. Longest chain 20 peptides. Score 0.526 Taking the results from Round 5 Chains 47, Residues 262, Estimated correctness of the model 19.6 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9151 restraints for refining 4228 atoms. 8013 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2824 (Rfree = 0.000) for 4228 atoms. Found 32 (37 requested) and removed 39 (18 requested) atoms. Cycle 17: After refmac, R = 0.2550 (Rfree = 0.000) for 4204 atoms. Found 24 (37 requested) and removed 25 (18 requested) atoms. Cycle 18: After refmac, R = 0.2483 (Rfree = 0.000) for 4189 atoms. Found 22 (37 requested) and removed 28 (18 requested) atoms. Cycle 19: After refmac, R = 0.2365 (Rfree = 0.000) for 4179 atoms. Found 17 (37 requested) and removed 23 (18 requested) atoms. Cycle 20: After refmac, R = 0.2368 (Rfree = 0.000) for 4166 atoms. Found 20 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 3.19 Search for helices and strands: 0 residues in 0 chains, 4289 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4309 seeds are put forward Round 1: 244 peptides, 46 chains. Longest chain 13 peptides. Score 0.348 Round 2: 278 peptides, 43 chains. Longest chain 19 peptides. Score 0.470 Round 3: 271 peptides, 39 chains. Longest chain 19 peptides. Score 0.496 Round 4: 299 peptides, 43 chains. Longest chain 18 peptides. Score 0.520 Round 5: 296 peptides, 45 chains. Longest chain 15 peptides. Score 0.493 Taking the results from Round 4 Chains 43, Residues 256, Estimated correctness of the model 17.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9600 restraints for refining 4229 atoms. 8619 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3128 (Rfree = 0.000) for 4229 atoms. Found 37 (37 requested) and removed 52 (18 requested) atoms. Cycle 22: After refmac, R = 0.2834 (Rfree = 0.000) for 4181 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. Cycle 23: After refmac, R = 0.2449 (Rfree = 0.000) for 4158 atoms. Found 26 (37 requested) and removed 20 (18 requested) atoms. Cycle 24: After refmac, R = 0.2118 (Rfree = 0.000) for 4143 atoms. Found 13 (37 requested) and removed 19 (18 requested) atoms. Cycle 25: After refmac, R = 0.2061 (Rfree = 0.000) for 4134 atoms. Found 5 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 4241 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 4266 seeds are put forward Round 1: 228 peptides, 45 chains. Longest chain 13 peptides. Score 0.315 Round 2: 272 peptides, 47 chains. Longest chain 12 peptides. Score 0.412 Round 3: 281 peptides, 45 chains. Longest chain 19 peptides. Score 0.456 Round 4: 259 peptides, 40 chains. Longest chain 14 peptides. Score 0.456 Round 5: 281 peptides, 44 chains. Longest chain 15 peptides. Score 0.467 Taking the results from Round 5 Chains 44, Residues 237, Estimated correctness of the model 0.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9300 restraints for refining 4168 atoms. 8396 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2443 (Rfree = 0.000) for 4168 atoms. Found 36 (37 requested) and removed 28 (18 requested) atoms. Cycle 27: After refmac, R = 0.2359 (Rfree = 0.000) for 4167 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2400 (Rfree = 0.000) for 4177 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. Cycle 29: After refmac, R = 0.2030 (Rfree = 0.000) for 4182 atoms. Found 10 (37 requested) and removed 20 (18 requested) atoms. Cycle 30: After refmac, R = 0.2004 (Rfree = 0.000) for 4166 atoms. Found 9 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 4294 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4310 seeds are put forward Round 1: 246 peptides, 47 chains. Longest chain 13 peptides. Score 0.342 Round 2: 264 peptides, 45 chains. Longest chain 12 peptides. Score 0.413 Round 3: 272 peptides, 41 chains. Longest chain 13 peptides. Score 0.477 Round 4: 270 peptides, 45 chains. Longest chain 14 peptides. Score 0.429 Round 5: 276 peptides, 41 chains. Longest chain 15 peptides. Score 0.487 Taking the results from Round 5 Chains 42, Residues 235, Estimated correctness of the model 7.1 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9272 restraints for refining 4229 atoms. 8328 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2511 (Rfree = 0.000) for 4229 atoms. Found 32 (37 requested) and removed 29 (18 requested) atoms. Cycle 32: After refmac, R = 0.2365 (Rfree = 0.000) for 4213 atoms. Found 28 (37 requested) and removed 20 (18 requested) atoms. Cycle 33: After refmac, R = 0.2325 (Rfree = 0.000) for 4216 atoms. Found 28 (37 requested) and removed 26 (18 requested) atoms. Cycle 34: After refmac, R = 0.1950 (Rfree = 0.000) for 4209 atoms. Found 10 (37 requested) and removed 24 (18 requested) atoms. Cycle 35: After refmac, R = 0.2059 (Rfree = 0.000) for 4186 atoms. Found 16 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 4305 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4318 seeds are put forward Round 1: 228 peptides, 45 chains. Longest chain 14 peptides. Score 0.315 Round 2: 250 peptides, 42 chains. Longest chain 15 peptides. Score 0.411 Round 3: 258 peptides, 41 chains. Longest chain 17 peptides. Score 0.442 Round 4: 280 peptides, 45 chains. Longest chain 15 peptides. Score 0.454 Round 5: 271 peptides, 42 chains. Longest chain 15 peptides. Score 0.464 Taking the results from Round 5 Chains 42, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9592 restraints for refining 4229 atoms. 8718 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2391 (Rfree = 0.000) for 4229 atoms. Found 31 (37 requested) and removed 23 (18 requested) atoms. Cycle 37: After refmac, R = 0.2279 (Rfree = 0.000) for 4228 atoms. Found 24 (38 requested) and removed 21 (19 requested) atoms. Cycle 38: After refmac, R = 0.2251 (Rfree = 0.000) for 4224 atoms. Found 24 (37 requested) and removed 26 (18 requested) atoms. Cycle 39: After refmac, R = 0.1945 (Rfree = 0.000) for 4216 atoms. Found 9 (37 requested) and removed 19 (18 requested) atoms. Cycle 40: After refmac, R = 0.1882 (Rfree = 0.000) for 4201 atoms. Found 7 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 4293 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4309 seeds are put forward Round 1: 222 peptides, 41 chains. Longest chain 16 peptides. Score 0.346 Round 2: 231 peptides, 37 chains. Longest chain 14 peptides. Score 0.418 Round 3: 225 peptides, 37 chains. Longest chain 17 peptides. Score 0.402 Round 4: 226 peptides, 34 chains. Longest chain 18 peptides. Score 0.440 Round 5: 223 peptides, 36 chains. Longest chain 16 peptides. Score 0.408 Taking the results from Round 4 Chains 34, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9708 restraints for refining 4229 atoms. 8974 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2332 (Rfree = 0.000) for 4229 atoms. Found 25 (37 requested) and removed 21 (18 requested) atoms. Cycle 42: After refmac, R = 0.2182 (Rfree = 0.000) for 4225 atoms. Found 32 (37 requested) and removed 20 (18 requested) atoms. Cycle 43: After refmac, R = 0.2182 (Rfree = 0.000) for 4228 atoms. Found 30 (38 requested) and removed 20 (19 requested) atoms. Cycle 44: After refmac, R = 0.2105 (Rfree = 0.000) for 4236 atoms. Found 24 (38 requested) and removed 21 (19 requested) atoms. Cycle 45: After refmac, R = 0.2124 (Rfree = 0.000) for 4233 atoms. Found 23 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 4344 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4367 seeds are put forward Round 1: 189 peptides, 38 chains. Longest chain 8 peptides. Score 0.287 Round 2: 202 peptides, 36 chains. Longest chain 13 peptides. Score 0.350 Round 3: 213 peptides, 38 chains. Longest chain 10 peptides. Score 0.357 Round 4: 213 peptides, 38 chains. Longest chain 13 peptides. Score 0.357 Round 5: 225 peptides, 39 chains. Longest chain 13 peptides. Score 0.378 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 186, 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 2gfg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10582 reflections ( 99.61 % complete ) and 9664 restraints for refining 4229 atoms. 8959 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2218 (Rfree = 0.000) for 4229 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2216 (Rfree = 0.000) for 4204 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2136 (Rfree = 0.000) for 4181 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2093 (Rfree = 0.000) for 4163 atoms. TimeTaking 52.3