Sun 23 Dec 22:23:08 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 2gfg-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.4-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/2gfg-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.4-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 22:23:18 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/2gfg-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.4-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 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-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: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-3.4-parrot-hancs.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 5160 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3568 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3032 (Rfree = 0.000) for 5160 atoms. Found 21 (38 requested) and removed 73 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 5193 seeds are put forward NCS extension: 0 residues added, 5193 seeds are put forward Round 1: 193 peptides, 39 chains. Longest chain 12 peptides. Score 0.286 Round 2: 249 peptides, 43 chains. Longest chain 11 peptides. Score 0.396 Round 3: 265 peptides, 42 chains. Longest chain 16 peptides. Score 0.449 Round 4: 284 peptides, 46 chains. Longest chain 17 peptides. Score 0.453 Round 5: 289 peptides, 45 chains. Longest chain 13 peptides. Score 0.476 Taking the results from Round 5 Chains 45, Residues 244, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9603 restraints for refining 4211 atoms. 8655 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2846 (Rfree = 0.000) for 4211 atoms. Found 19 (31 requested) and removed 31 (15 requested) atoms. Cycle 2: After refmac, R = 0.2656 (Rfree = 0.000) for 4162 atoms. Found 17 (31 requested) and removed 23 (15 requested) atoms. Cycle 3: After refmac, R = 0.2558 (Rfree = 0.000) for 4147 atoms. Found 11 (31 requested) and removed 19 (15 requested) atoms. Cycle 4: After refmac, R = 0.2575 (Rfree = 0.000) for 4133 atoms. Found 10 (31 requested) and removed 31 (15 requested) atoms. Cycle 5: After refmac, R = 0.2499 (Rfree = 0.000) for 4100 atoms. Found 5 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 4229 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4245 seeds are put forward Round 1: 246 peptides, 46 chains. Longest chain 10 peptides. Score 0.353 Round 2: 278 peptides, 46 chains. Longest chain 14 peptides. Score 0.438 Round 3: 289 peptides, 43 chains. Longest chain 15 peptides. Score 0.497 Round 4: 298 peptides, 41 chains. Longest chain 13 peptides. Score 0.537 Round 5: 301 peptides, 47 chains. Longest chain 14 peptides. Score 0.484 Taking the results from Round 4 Chains 42, Residues 257, Estimated correctness of the model 6.8 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9552 restraints for refining 4212 atoms. 8501 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2747 (Rfree = 0.000) for 4212 atoms. Found 22 (31 requested) and removed 25 (15 requested) atoms. Cycle 7: After refmac, R = 0.2807 (Rfree = 0.000) for 4199 atoms. Found 13 (31 requested) and removed 30 (15 requested) atoms. Cycle 8: After refmac, R = 0.2531 (Rfree = 0.000) for 4156 atoms. Found 20 (31 requested) and removed 19 (15 requested) atoms. Cycle 9: After refmac, R = 0.2504 (Rfree = 0.000) for 4141 atoms. Found 20 (31 requested) and removed 22 (15 requested) atoms. Cycle 10: After refmac, R = 0.2359 (Rfree = 0.000) for 4132 atoms. Found 12 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 4275 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4289 seeds are put forward Round 1: 261 peptides, 49 chains. Longest chain 11 peptides. Score 0.360 Round 2: 272 peptides, 43 chains. Longest chain 13 peptides. Score 0.456 Round 3: 286 peptides, 49 chains. Longest chain 12 peptides. Score 0.426 Round 4: 296 peptides, 45 chains. Longest chain 13 peptides. Score 0.493 Round 5: 301 peptides, 46 chains. Longest chain 14 peptides. Score 0.494 Taking the results from Round 5 Chains 46, Residues 255, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9628 restraints for refining 4211 atoms. 8654 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2455 (Rfree = 0.000) for 4211 atoms. Found 20 (31 requested) and removed 17 (15 requested) atoms. Cycle 12: After refmac, R = 0.2551 (Rfree = 0.000) for 4197 atoms. Found 14 (31 requested) and removed 30 (15 requested) atoms. Cycle 13: After refmac, R = 0.2245 (Rfree = 0.000) for 4167 atoms. Found 13 (31 requested) and removed 29 (15 requested) atoms. Cycle 14: After refmac, R = 0.2296 (Rfree = 0.000) for 4129 atoms. Found 21 (31 requested) and removed 23 (15 requested) atoms. Cycle 15: After refmac, R = 0.2571 (Rfree = 0.000) for 4121 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 4291 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4303 seeds are put forward Round 1: 253 peptides, 49 chains. Longest chain 10 peptides. Score 0.338 Round 2: 283 peptides, 44 chains. Longest chain 17 peptides. Score 0.472 Round 3: 304 peptides, 49 chains. Longest chain 13 peptides. Score 0.470 Round 4: 298 peptides, 47 chains. Longest chain 19 peptides. Score 0.477 Round 5: 298 peptides, 43 chains. Longest chain 19 peptides. Score 0.518 Taking the results from Round 5 Chains 43, Residues 255, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8848 reflections ( 99.54 % complete ) and 9446 restraints for refining 4212 atoms. 8443 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2513 (Rfree = 0.000) for 4212 atoms. Found 21 (31 requested) and removed 25 (15 requested) atoms. Cycle 17: After refmac, R = 0.2518 (Rfree = 0.000) for 4185 atoms. Found 14 (31 requested) and removed 25 (15 requested) atoms. Cycle 18: After refmac, R = 0.2195 (Rfree = 0.000) for 4162 atoms. Found 9 (31 requested) and removed 18 (15 requested) atoms. Cycle 19: After refmac, R = 0.2316 (Rfree = 0.000) for 4150 atoms. Found 13 (31 requested) and removed 26 (15 requested) atoms. Cycle 20: After refmac, R = 0.2197 (Rfree = 0.000) for 4135 atoms. Found 5 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 4275 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 4300 seeds are put forward Round 1: 254 peptides, 49 chains. Longest chain 10 peptides. Score 0.340 Round 2: 283 peptides, 48 chains. Longest chain 13 peptides. Score 0.429 Round 3: 282 peptides, 45 chains. Longest chain 24 peptides. Score 0.459 Round 4: 271 peptides, 42 chains. Longest chain 19 peptides. Score 0.464 Round 5: 276 peptides, 40 chains. Longest chain 18 peptides. Score 0.497 Taking the results from Round 5 Chains 40, Residues 236, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9693 restraints for refining 4212 atoms. 8759 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2421 (Rfree = 0.000) for 4212 atoms. Found 21 (31 requested) and removed 18 (15 requested) atoms. Cycle 22: After refmac, R = 0.2362 (Rfree = 0.000) for 4200 atoms. Found 15 (31 requested) and removed 25 (15 requested) atoms. Cycle 23: After refmac, R = 0.2135 (Rfree = 0.000) for 4172 atoms. Found 11 (31 requested) and removed 17 (15 requested) atoms. Cycle 24: After refmac, R = 0.2133 (Rfree = 0.000) for 4161 atoms. Found 6 (31 requested) and removed 15 (15 requested) atoms. Cycle 25: After refmac, R = 0.2116 (Rfree = 0.000) for 4145 atoms. Found 7 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 4238 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 4265 seeds are put forward Round 1: 228 peptides, 45 chains. Longest chain 13 peptides. Score 0.315 Round 2: 278 peptides, 47 chains. Longest chain 15 peptides. Score 0.427 Round 3: 283 peptides, 48 chains. Longest chain 15 peptides. Score 0.429 Round 4: 299 peptides, 47 chains. Longest chain 17 peptides. Score 0.479 Round 5: 278 peptides, 42 chains. Longest chain 17 peptides. Score 0.481 Taking the results from Round 5 Chains 42, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9590 restraints for refining 4211 atoms. 8688 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2404 (Rfree = 0.000) for 4211 atoms. Found 26 (31 requested) and removed 20 (15 requested) atoms. Cycle 27: After refmac, R = 0.2338 (Rfree = 0.000) for 4204 atoms. Found 8 (31 requested) and removed 17 (15 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Cycle 28: After refmac, R = 0.2176 (Rfree = 0.000) for 4186 atoms. Found 7 (31 requested) and removed 21 (15 requested) atoms. Cycle 29: After refmac, R = 0.2238 (Rfree = 0.000) for 4167 atoms. Found 6 (31 requested) and removed 17 (15 requested) atoms. Cycle 30: After refmac, R = 0.2114 (Rfree = 0.000) for 4154 atoms. Found 8 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 4279 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4294 seeds are put forward Round 1: 220 peptides, 40 chains. Longest chain 13 peptides. Score 0.352 Round 2: 263 peptides, 41 chains. Longest chain 18 peptides. Score 0.455 Round 3: 279 peptides, 43 chains. Longest chain 14 peptides. Score 0.473 Round 4: 264 peptides, 40 chains. Longest chain 19 peptides. Score 0.468 Round 5: 262 peptides, 42 chains. Longest chain 14 peptides. Score 0.442 Taking the results from Round 3 Chains 43, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9356 restraints for refining 4212 atoms. 8455 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2714 (Rfree = 0.000) for 4212 atoms. Found 20 (31 requested) and removed 22 (15 requested) atoms. Cycle 32: After refmac, R = 0.2240 (Rfree = 0.000) for 4194 atoms. Found 11 (31 requested) and removed 20 (15 requested) atoms. Cycle 33: After refmac, R = 0.2183 (Rfree = 0.000) for 4176 atoms. Found 9 (31 requested) and removed 16 (15 requested) atoms. Cycle 34: After refmac, R = 0.2086 (Rfree = 0.000) for 4162 atoms. Found 9 (31 requested) and removed 17 (15 requested) atoms. Cycle 35: After refmac, R = 0.2097 (Rfree = 0.000) for 4147 atoms. Found 6 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 4256 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4271 seeds are put forward Round 1: 236 peptides, 46 chains. Longest chain 11 peptides. Score 0.325 Round 2: 258 peptides, 44 chains. Longest chain 16 peptides. Score 0.409 Round 3: 261 peptides, 41 chains. Longest chain 16 peptides. Score 0.450 Round 4: 266 peptides, 41 chains. Longest chain 16 peptides. Score 0.462 Round 5: 269 peptides, 42 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 4 Chains 41, Residues 225, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9487 restraints for refining 4211 atoms. 8603 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2338 (Rfree = 0.000) for 4211 atoms. Found 20 (31 requested) and removed 17 (15 requested) atoms. Cycle 37: After refmac, R = 0.2243 (Rfree = 0.000) for 4202 atoms. Found 9 (31 requested) and removed 21 (15 requested) atoms. Cycle 38: After refmac, R = 0.2152 (Rfree = 0.000) for 4185 atoms. Found 7 (31 requested) and removed 17 (15 requested) atoms. Cycle 39: After refmac, R = 0.2451 (Rfree = 0.000) for 4169 atoms. Found 11 (31 requested) and removed 26 (15 requested) atoms. Cycle 40: After refmac, R = 0.2155 (Rfree = 0.000) for 4144 atoms. Found 9 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 4251 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 4263 seeds are put forward Round 1: 229 peptides, 48 chains. Longest chain 13 peptides. Score 0.281 Round 2: 250 peptides, 41 chains. Longest chain 13 peptides. Score 0.422 Round 3: 249 peptides, 45 chains. Longest chain 13 peptides. Score 0.373 Round 4: 251 peptides, 44 chains. Longest chain 13 peptides. Score 0.390 Round 5: 252 peptides, 40 chains. Longest chain 13 peptides. Score 0.438 Taking the results from Round 5 Chains 40, Residues 212, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8848 reflections ( 99.54 % complete ) and 9546 restraints for refining 4211 atoms. 8708 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2379 (Rfree = 0.000) for 4211 atoms. Found 15 (31 requested) and removed 22 (15 requested) atoms. Cycle 42: After refmac, R = 0.2449 (Rfree = 0.000) for 4187 atoms. Found 29 (31 requested) and removed 19 (15 requested) atoms. Cycle 43: After refmac, R = 0.2274 (Rfree = 0.000) for 4177 atoms. Found 20 (31 requested) and removed 22 (15 requested) atoms. Cycle 44: After refmac, R = 0.1968 (Rfree = 0.000) for 4168 atoms. Found 4 (31 requested) and removed 17 (15 requested) atoms. Cycle 45: After refmac, R = 0.1963 (Rfree = 0.000) for 4150 atoms. Found 10 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 4260 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4276 seeds are put forward Round 1: 206 peptides, 43 chains. Longest chain 12 peptides. Score 0.274 Round 2: 236 peptides, 42 chains. Longest chain 13 peptides. Score 0.373 Round 3: 245 peptides, 41 chains. Longest chain 17 peptides. Score 0.409 Round 4: 236 peptides, 39 chains. Longest chain 18 peptides. Score 0.408 Round 5: 241 peptides, 40 chains. Longest chain 14 peptides. Score 0.410 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 201, 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. 8848 reflections ( 99.54 % complete ) and 9631 restraints for refining 4212 atoms. 8867 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2396 (Rfree = 0.000) for 4212 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2353 (Rfree = 0.000) for 4180 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1833 (Rfree = 0.000) for 4157 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1699 (Rfree = 0.000) for 4138 atoms. TimeTaking 62.08