Mon 24 Dec 00:39:18 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-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/2gfg-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-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 00:39:23 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-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 415 and 0 Target number of residues in the AU: 415 Target solvent content: 0.6285 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-3.4-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: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-3.4-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 3.400 Wilson plot Bfac: 65.65 8848 reflections ( 99.54 % complete ) and 0 restraints for refining 5101 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3564 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3095 (Rfree = 0.000) for 5101 atoms. Found 33 (38 requested) and removed 48 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 5162 seeds are put forward NCS extension: 0 residues added, 5162 seeds are put forward Round 1: 214 peptides, 43 chains. Longest chain 10 peptides. Score 0.298 Round 2: 284 peptides, 49 chains. Longest chain 13 peptides. Score 0.421 Round 3: 301 peptides, 46 chains. Longest chain 17 peptides. Score 0.494 Round 4: 303 peptides, 40 chains. Longest chain 22 peptides. Score 0.558 Round 5: 307 peptides, 44 chains. Longest chain 19 peptides. Score 0.528 Taking the results from Round 4 Chains 42, Residues 263, Estimated correctness of the model 14.4 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9309 restraints for refining 4212 atoms. 8232 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2825 (Rfree = 0.000) for 4212 atoms. Found 25 (31 requested) and removed 30 (15 requested) atoms. Cycle 2: After refmac, R = 0.2638 (Rfree = 0.000) for 4160 atoms. Found 16 (31 requested) and removed 30 (15 requested) atoms. Cycle 3: After refmac, R = 0.2553 (Rfree = 0.000) for 4114 atoms. Found 16 (31 requested) and removed 21 (15 requested) atoms. Cycle 4: After refmac, R = 0.2359 (Rfree = 0.000) for 4091 atoms. Found 10 (31 requested) and removed 18 (15 requested) atoms. Cycle 5: After refmac, R = 0.2358 (Rfree = 0.000) for 4063 atoms. Found 11 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 4191 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 4210 seeds are put forward Round 1: 288 peptides, 51 chains. Longest chain 13 peptides. Score 0.409 Round 2: 310 peptides, 45 chains. Longest chain 21 peptides. Score 0.525 Round 3: 320 peptides, 44 chains. Longest chain 18 peptides. Score 0.556 Round 4: 314 peptides, 43 chains. Longest chain 21 peptides. Score 0.553 Round 5: 316 peptides, 45 chains. Longest chain 21 peptides. Score 0.538 Taking the results from Round 3 Chains 45, Residues 276, Estimated correctness of the model 13.7 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9200 restraints for refining 4148 atoms. 8098 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2513 (Rfree = 0.000) for 4148 atoms. Found 23 (31 requested) and removed 24 (15 requested) atoms. Cycle 7: After refmac, R = 0.2317 (Rfree = 0.000) for 4125 atoms. Found 18 (31 requested) and removed 17 (15 requested) atoms. Cycle 8: After refmac, R = 0.2238 (Rfree = 0.000) for 4105 atoms. Found 13 (31 requested) and removed 26 (15 requested) atoms. Cycle 9: After refmac, R = 0.2309 (Rfree = 0.000) for 4080 atoms. Found 12 (30 requested) and removed 21 (15 requested) atoms. Cycle 10: After refmac, R = 0.2199 (Rfree = 0.000) for 4063 atoms. Found 22 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 4240 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4255 seeds are put forward Round 1: 256 peptides, 47 chains. Longest chain 13 peptides. Score 0.369 Round 2: 293 peptides, 48 chains. Longest chain 16 peptides. Score 0.454 Round 3: 290 peptides, 45 chains. Longest chain 15 peptides. Score 0.478 Round 4: 285 peptides, 42 chains. Longest chain 18 peptides. Score 0.498 Round 5: 295 peptides, 44 chains. Longest chain 19 peptides. Score 0.501 Taking the results from Round 5 Chains 44, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9652 restraints for refining 4212 atoms. 8692 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2262 (Rfree = 0.000) for 4212 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 12: After refmac, R = 0.2118 (Rfree = 0.000) for 4195 atoms. Found 14 (31 requested) and removed 16 (15 requested) atoms. Cycle 13: After refmac, R = 0.2061 (Rfree = 0.000) for 4187 atoms. Found 17 (31 requested) and removed 18 (15 requested) atoms. Cycle 14: After refmac, R = 0.1903 (Rfree = 0.000) for 4174 atoms. Found 9 (31 requested) and removed 16 (15 requested) atoms. Cycle 15: After refmac, R = 0.1830 (Rfree = 0.000) for 4166 atoms. Found 9 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 4298 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 4314 seeds are put forward Round 1: 244 peptides, 49 chains. Longest chain 10 peptides. Score 0.312 Round 2: 272 peptides, 42 chains. Longest chain 18 peptides. Score 0.466 Round 3: 274 peptides, 45 chains. Longest chain 11 peptides. Score 0.439 Round 4: 269 peptides, 44 chains. Longest chain 12 peptides. Score 0.437 Round 5: 296 peptides, 40 chains. Longest chain 23 peptides. Score 0.543 Taking the results from Round 5 Chains 40, Residues 256, Estimated correctness of the model 9.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9444 restraints for refining 4212 atoms. 8460 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2173 (Rfree = 0.000) for 4212 atoms. Found 21 (31 requested) and removed 17 (15 requested) atoms. Cycle 17: After refmac, R = 0.2170 (Rfree = 0.000) for 4193 atoms. Found 17 (31 requested) and removed 21 (15 requested) atoms. Cycle 18: After refmac, R = 0.1944 (Rfree = 0.000) for 4176 atoms. Found 11 (31 requested) and removed 17 (15 requested) atoms. Cycle 19: After refmac, R = 0.1917 (Rfree = 0.000) for 4154 atoms. Found 16 (31 requested) and removed 15 (15 requested) atoms. Cycle 20: After refmac, R = 0.1912 (Rfree = 0.000) for 4151 atoms. Found 16 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 4300 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 4333 seeds are put forward Round 1: 260 peptides, 53 chains. Longest chain 9 peptides. Score 0.310 Round 2: 283 peptides, 48 chains. Longest chain 24 peptides. Score 0.429 Round 3: 285 peptides, 46 chains. Longest chain 13 peptides. Score 0.456 Round 4: 269 peptides, 42 chains. Longest chain 18 peptides. Score 0.459 Round 5: 287 peptides, 44 chains. Longest chain 25 peptides. Score 0.482 Taking the results from Round 5 Chains 44, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9416 restraints for refining 4212 atoms. 8488 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2765 (Rfree = 0.000) for 4212 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 22: After refmac, R = 0.2175 (Rfree = 0.000) for 4186 atoms. Found 21 (31 requested) and removed 21 (15 requested) atoms. Cycle 23: After refmac, R = 0.2147 (Rfree = 0.000) for 4170 atoms. Found 31 (31 requested) and removed 15 (15 requested) atoms. Cycle 24: After refmac, R = 0.2145 (Rfree = 0.000) for 4174 atoms. Found 31 (31 requested) and removed 20 (15 requested) atoms. Cycle 25: After refmac, R = 0.2380 (Rfree = 0.000) for 4168 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 4333 seeds are put forward NCS extension: 46 residues added (1 deleted due to clashes), 4379 seeds are put forward Round 1: 225 peptides, 46 chains. Longest chain 16 peptides. Score 0.294 Round 2: 256 peptides, 48 chains. Longest chain 11 peptides. Score 0.358 Round 3: 289 peptides, 47 chains. Longest chain 20 peptides. Score 0.455 Round 4: 288 peptides, 45 chains. Longest chain 17 peptides. Score 0.474 Round 5: 290 peptides, 46 chains. Longest chain 20 peptides. Score 0.468 Taking the results from Round 4 Chains 45, Residues 243, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9238 restraints for refining 4200 atoms. 8242 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2352 (Rfree = 0.000) for 4200 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 27: After refmac, R = 0.2429 (Rfree = 0.000) for 4186 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 28: After refmac, R = 0.2602 (Rfree = 0.000) for 4178 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 29: After refmac, R = 0.2188 (Rfree = 0.000) for 4159 atoms. Found 29 (31 requested) and removed 21 (15 requested) atoms. Cycle 30: After refmac, R = 0.1736 (Rfree = 0.000) for 4161 atoms. Found 11 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 4263 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 4283 seeds are put forward Round 1: 205 peptides, 40 chains. Longest chain 11 peptides. Score 0.309 Round 2: 249 peptides, 41 chains. Longest chain 12 peptides. Score 0.419 Round 3: 260 peptides, 42 chains. Longest chain 16 peptides. Score 0.436 Round 4: 265 peptides, 41 chains. Longest chain 16 peptides. Score 0.460 Round 5: 282 peptides, 42 chains. Longest chain 18 peptides. Score 0.491 Taking the results from Round 5 Chains 42, Residues 240, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9353 restraints for refining 4212 atoms. 8435 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2202 (Rfree = 0.000) for 4212 atoms. Found 23 (31 requested) and removed 22 (15 requested) atoms. Cycle 32: After refmac, R = 0.2053 (Rfree = 0.000) for 4196 atoms. Found 26 (31 requested) and removed 20 (15 requested) atoms. Cycle 33: After refmac, R = 0.1981 (Rfree = 0.000) for 4191 atoms. Found 22 (31 requested) and removed 18 (15 requested) atoms. Cycle 34: After refmac, R = 0.1891 (Rfree = 0.000) for 4190 atoms. Found 14 (31 requested) and removed 17 (15 requested) atoms. Cycle 35: After refmac, R = 0.1777 (Rfree = 0.000) for 4181 atoms. Found 14 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 4295 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 4321 seeds are put forward Round 1: 214 peptides, 41 chains. Longest chain 10 peptides. Score 0.323 Round 2: 254 peptides, 44 chains. Longest chain 11 peptides. Score 0.398 Round 3: 244 peptides, 41 chains. Longest chain 12 peptides. Score 0.406 Round 4: 256 peptides, 41 chains. Longest chain 15 peptides. Score 0.437 Round 5: 250 peptides, 40 chains. Longest chain 16 peptides. Score 0.433 Taking the results from Round 4 Chains 41, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9410 restraints for refining 4212 atoms. 8591 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2083 (Rfree = 0.000) for 4212 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 37: After refmac, R = 0.1966 (Rfree = 0.000) for 4212 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. Cycle 38: After refmac, R = 0.1836 (Rfree = 0.000) for 4221 atoms. Found 18 (31 requested) and removed 18 (15 requested) atoms. Cycle 39: After refmac, R = 0.1816 (Rfree = 0.000) for 4213 atoms. Found 22 (31 requested) and removed 17 (15 requested) atoms. Cycle 40: After refmac, R = 0.1788 (Rfree = 0.000) for 4210 atoms. Found 16 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 4326 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4342 seeds are put forward Round 1: 209 peptides, 42 chains. Longest chain 11 peptides. Score 0.296 Round 2: 243 peptides, 42 chains. Longest chain 15 peptides. Score 0.392 Round 3: 257 peptides, 45 chains. Longest chain 16 peptides. Score 0.395 Round 4: 254 peptides, 42 chains. Longest chain 14 peptides. Score 0.421 Round 5: 262 peptides, 41 chains. Longest chain 18 peptides. Score 0.453 Taking the results from Round 5 Chains 41, Residues 221, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9346 restraints for refining 4212 atoms. 8483 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2111 (Rfree = 0.000) for 4212 atoms. Found 26 (31 requested) and removed 18 (15 requested) atoms. Cycle 42: After refmac, R = 0.1951 (Rfree = 0.000) for 4207 atoms. Found 20 (31 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.1786 (Rfree = 0.000) for 4203 atoms. Found 16 (31 requested) and removed 16 (15 requested) atoms. Cycle 44: After refmac, R = 0.1748 (Rfree = 0.000) for 4197 atoms. Found 14 (31 requested) and removed 19 (15 requested) atoms. Cycle 45: After refmac, R = 0.1773 (Rfree = 0.000) for 4187 atoms. Found 19 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 4290 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4307 seeds are put forward Round 1: 206 peptides, 43 chains. Longest chain 10 peptides. Score 0.274 Round 2: 240 peptides, 40 chains. Longest chain 13 peptides. Score 0.407 Round 3: 240 peptides, 40 chains. Longest chain 13 peptides. Score 0.407 Round 4: 250 peptides, 37 chains. Longest chain 17 peptides. Score 0.467 Round 5: 231 peptides, 38 chains. Longest chain 15 peptides. Score 0.406 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 213, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2gfg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8848 reflections ( 99.54 % complete ) and 9436 restraints for refining 4212 atoms. 8596 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2022 (Rfree = 0.000) for 4212 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.1905 (Rfree = 0.000) for 4191 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1891 (Rfree = 0.000) for 4170 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1852 (Rfree = 0.000) for 4149 atoms. TimeTaking 54.15