Mon 24 Dec 00:22:11 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-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/2gfg-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-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 ============================================================ Mon 24 Dec 00:22:16 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-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 401 and 0 Target number of residues in the AU: 401 Target solvent content: 0.6411 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-3.6-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: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-3.6-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 3.600 Wilson plot Bfac: 72.38 7478 reflections ( 99.45 % complete ) and 0 restraints for refining 5150 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3588 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3416 (Rfree = 0.000) for 5150 atoms. Found 33 (33 requested) and removed 58 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 5216 seeds are put forward NCS extension: 0 residues added, 5216 seeds are put forward Round 1: 215 peptides, 43 chains. Longest chain 12 peptides. Score 0.301 Round 2: 263 peptides, 44 chains. Longest chain 19 peptides. Score 0.422 Round 3: 281 peptides, 41 chains. Longest chain 20 peptides. Score 0.499 Round 4: 291 peptides, 45 chains. Longest chain 18 peptides. Score 0.481 Round 5: 290 peptides, 43 chains. Longest chain 20 peptides. Score 0.499 Taking the results from Round 5 Chains 43, Residues 247, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9827 restraints for refining 4198 atoms. 8856 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2903 (Rfree = 0.000) for 4198 atoms. Found 24 (26 requested) and removed 36 (13 requested) atoms. Cycle 2: After refmac, R = 0.2739 (Rfree = 0.000) for 4133 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 3: After refmac, R = 0.2629 (Rfree = 0.000) for 4096 atoms. Found 24 (26 requested) and removed 26 (13 requested) atoms. Cycle 4: After refmac, R = 0.2514 (Rfree = 0.000) for 4067 atoms. Found 24 (26 requested) and removed 24 (13 requested) atoms. Cycle 5: After refmac, R = 0.2427 (Rfree = 0.000) for 4047 atoms. Found 20 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 4197 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4216 seeds are put forward Round 1: 242 peptides, 48 chains. Longest chain 9 peptides. Score 0.319 Round 2: 265 peptides, 46 chains. Longest chain 13 peptides. Score 0.405 Round 3: 284 peptides, 49 chains. Longest chain 13 peptides. Score 0.421 Round 4: 271 peptides, 46 chains. Longest chain 12 peptides. Score 0.420 Round 5: 289 peptides, 40 chains. Longest chain 18 peptides. Score 0.527 Taking the results from Round 5 Chains 40, Residues 249, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9662 restraints for refining 4199 atoms. 8667 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2836 (Rfree = 0.000) for 4199 atoms. Found 19 (26 requested) and removed 44 (13 requested) atoms. Cycle 7: After refmac, R = 0.2545 (Rfree = 0.000) for 4148 atoms. Found 16 (26 requested) and removed 33 (13 requested) atoms. Cycle 8: After refmac, R = 0.2507 (Rfree = 0.000) for 4106 atoms. Found 24 (26 requested) and removed 35 (13 requested) atoms. Cycle 9: After refmac, R = 0.2171 (Rfree = 0.000) for 4086 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. Cycle 10: After refmac, R = 0.2113 (Rfree = 0.000) for 4065 atoms. Found 6 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 4215 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4235 seeds are put forward Round 1: 236 peptides, 47 chains. Longest chain 10 peptides. Score 0.313 Round 2: 267 peptides, 40 chains. Longest chain 13 peptides. Score 0.476 Round 3: 279 peptides, 44 chains. Longest chain 11 peptides. Score 0.462 Round 4: 284 peptides, 43 chains. Longest chain 15 peptides. Score 0.485 Round 5: 286 peptides, 45 chains. Longest chain 17 peptides. Score 0.469 Taking the results from Round 4 Chains 43, Residues 241, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9667 restraints for refining 4199 atoms. 8689 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2428 (Rfree = 0.000) for 4199 atoms. Found 24 (26 requested) and removed 28 (13 requested) atoms. Cycle 12: After refmac, R = 0.2316 (Rfree = 0.000) for 4165 atoms. Found 21 (26 requested) and removed 25 (13 requested) atoms. Cycle 13: After refmac, R = 0.2349 (Rfree = 0.000) for 4138 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. Cycle 14: After refmac, R = 0.2224 (Rfree = 0.000) for 4122 atoms. Found 22 (26 requested) and removed 27 (13 requested) atoms. Cycle 15: After refmac, R = 0.1955 (Rfree = 0.000) for 4112 atoms. Found 5 (26 requested) and removed 37 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 4247 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4267 seeds are put forward Round 1: 236 peptides, 44 chains. Longest chain 13 peptides. Score 0.349 Round 2: 247 peptides, 38 chains. Longest chain 20 peptides. Score 0.448 Round 3: 242 peptides, 38 chains. Longest chain 11 peptides. Score 0.435 Round 4: 246 peptides, 36 chains. Longest chain 14 peptides. Score 0.468 Round 5: 251 peptides, 38 chains. Longest chain 12 peptides. Score 0.458 Taking the results from Round 4 Chains 36, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9914 restraints for refining 4198 atoms. 9110 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2479 (Rfree = 0.000) for 4198 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. Cycle 17: After refmac, R = 0.2441 (Rfree = 0.000) for 4175 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. Cycle 18: After refmac, R = 0.2493 (Rfree = 0.000) for 4156 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 19: After refmac, R = 0.2257 (Rfree = 0.000) for 4137 atoms. Found 21 (26 requested) and removed 20 (13 requested) atoms. Cycle 20: After refmac, R = 0.1857 (Rfree = 0.000) for 4123 atoms. Found 4 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 4244 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4262 seeds are put forward Round 1: 216 peptides, 44 chains. Longest chain 9 peptides. Score 0.292 Round 2: 267 peptides, 46 chains. Longest chain 11 peptides. Score 0.410 Round 3: 263 peptides, 42 chains. Longest chain 12 peptides. Score 0.444 Round 4: 250 peptides, 38 chains. Longest chain 14 peptides. Score 0.456 Round 5: 255 peptides, 38 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 5 Chains 38, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9701 restraints for refining 4198 atoms. 8871 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2402 (Rfree = 0.000) for 4198 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2446 (Rfree = 0.000) for 4175 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 23: After refmac, R = 0.2318 (Rfree = 0.000) for 4155 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 24: After refmac, R = 0.1849 (Rfree = 0.000) for 4141 atoms. Found 7 (26 requested) and removed 16 (13 requested) atoms. Cycle 25: After refmac, R = 0.1809 (Rfree = 0.000) for 4125 atoms. Found 8 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 4241 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4255 seeds are put forward Round 1: 191 peptides, 39 chains. Longest chain 13 peptides. Score 0.280 Round 2: 218 peptides, 40 chains. Longest chain 13 peptides. Score 0.347 Round 3: 227 peptides, 39 chains. Longest chain 14 peptides. Score 0.384 Round 4: 242 peptides, 41 chains. Longest chain 13 peptides. Score 0.401 Round 5: 243 peptides, 42 chains. Longest chain 13 peptides. Score 0.392 Taking the results from Round 4 Chains 41, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9817 restraints for refining 4199 atoms. 9054 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2213 (Rfree = 0.000) for 4199 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 27: After refmac, R = 0.2078 (Rfree = 0.000) for 4175 atoms. Found 23 (26 requested) and removed 19 (13 requested) atoms. Cycle 28: After refmac, R = 0.2065 (Rfree = 0.000) for 4175 atoms. Found 22 (26 requested) and removed 23 (13 requested) atoms. Cycle 29: After refmac, R = 0.1985 (Rfree = 0.000) for 4169 atoms. Found 19 (26 requested) and removed 16 (13 requested) atoms. Cycle 30: After refmac, R = 0.1972 (Rfree = 0.000) for 4170 atoms. Found 16 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 4319 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4334 seeds are put forward Round 1: 201 peptides, 39 chains. Longest chain 11 peptides. Score 0.310 Round 2: 232 peptides, 40 chains. Longest chain 12 peptides. Score 0.386 Round 3: 239 peptides, 42 chains. Longest chain 12 peptides. Score 0.381 Round 4: 244 peptides, 41 chains. Longest chain 14 peptides. Score 0.406 Round 5: 236 peptides, 38 chains. Longest chain 13 peptides. Score 0.420 Taking the results from Round 5 Chains 38, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9948 restraints for refining 4199 atoms. 9194 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2172 (Rfree = 0.000) for 4199 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 32: After refmac, R = 0.2042 (Rfree = 0.000) for 4191 atoms. Found 26 (26 requested) and removed 16 (13 requested) atoms. Cycle 33: After refmac, R = 0.1939 (Rfree = 0.000) for 4194 atoms. Found 26 (26 requested) and removed 15 (13 requested) atoms. Cycle 34: After refmac, R = 0.1650 (Rfree = 0.000) for 4197 atoms. Found 5 (26 requested) and removed 14 (13 requested) atoms. Cycle 35: After refmac, R = 0.1608 (Rfree = 0.000) for 4182 atoms. Found 6 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 4307 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4327 seeds are put forward Round 1: 164 peptides, 35 chains. Longest chain 8 peptides. Score 0.248 Round 2: 204 peptides, 39 chains. Longest chain 12 peptides. Score 0.319 Round 3: 204 peptides, 37 chains. Longest chain 10 peptides. Score 0.344 Round 4: 199 peptides, 36 chains. Longest chain 10 peptides. Score 0.342 Round 5: 200 peptides, 34 chains. Longest chain 13 peptides. Score 0.369 Taking the results from Round 5 Chains 34, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 10256 restraints for refining 4199 atoms. 9626 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2085 (Rfree = 0.000) for 4199 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 37: After refmac, R = 0.2088 (Rfree = 0.000) for 4188 atoms. Found 26 (26 requested) and removed 16 (13 requested) atoms. Cycle 38: After refmac, R = 0.2028 (Rfree = 0.000) for 4186 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 39: After refmac, R = 0.2144 (Rfree = 0.000) for 4180 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 40: After refmac, R = 0.2083 (Rfree = 0.000) for 4180 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 4285 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4300 seeds are put forward Round 1: 168 peptides, 36 chains. Longest chain 9 peptides. Score 0.247 Round 2: 171 peptides, 33 chains. Longest chain 9 peptides. Score 0.297 Round 3: 183 peptides, 35 chains. Longest chain 11 peptides. Score 0.307 Round 4: 181 peptides, 30 chains. Longest chain 11 peptides. Score 0.365 Round 5: 184 peptides, 33 chains. Longest chain 10 peptides. Score 0.336 Taking the results from Round 4 Chains 30, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 10148 restraints for refining 4199 atoms. 9574 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2280 (Rfree = 0.000) for 4199 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 42: After refmac, R = 0.2197 (Rfree = 0.000) for 4187 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 43: After refmac, R = 0.2291 (Rfree = 0.000) for 4184 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 44: After refmac, R = 0.1866 (Rfree = 0.000) for 4178 atoms. Found 19 (26 requested) and removed 18 (13 requested) atoms. Cycle 45: After refmac, R = 0.1757 (Rfree = 0.000) for 4168 atoms. Found 16 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 4272 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4285 seeds are put forward Round 1: 168 peptides, 35 chains. Longest chain 11 peptides. Score 0.261 Round 2: 201 peptides, 37 chains. Longest chain 11 peptides. Score 0.335 Round 3: 195 peptides, 36 chains. Longest chain 9 peptides. Score 0.330 Round 4: 204 peptides, 37 chains. Longest chain 12 peptides. Score 0.344 Round 5: 206 peptides, 38 chains. Longest chain 10 peptides. Score 0.337 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 167, 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. 7478 reflections ( 99.45 % complete ) and 9918 restraints for refining 4178 atoms. 9287 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2226 (Rfree = 0.000) for 4178 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2295 (Rfree = 0.000) for 4154 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2322 (Rfree = 0.000) for 4134 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2186 (Rfree = 0.000) for 4117 atoms. TimeTaking 51.72