Sun 23 Dec 22:22:46 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 2f4p-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-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/2f4p-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-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 22:22:56 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/2f4p-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-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 396 and 0 Target number of residues in the AU: 396 Target solvent content: 0.6176 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 4704 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: 21.543 3.400 Wilson plot Bfac: 59.95 7529 reflections ( 99.56 % complete ) and 0 restraints for refining 5214 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3234 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3437 (Rfree = 0.000) for 5214 atoms. Found 39 (39 requested) and removed 70 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.69 Search for helices and strands: 0 residues in 0 chains, 5251 seeds are put forward NCS extension: 0 residues added, 5251 seeds are put forward Round 1: 214 peptides, 42 chains. Longest chain 9 peptides. Score 0.319 Round 2: 277 peptides, 47 chains. Longest chain 22 peptides. Score 0.440 Round 3: 314 peptides, 48 chains. Longest chain 16 peptides. Score 0.523 Round 4: 323 peptides, 43 chains. Longest chain 17 peptides. Score 0.593 Round 5: 335 peptides, 48 chains. Longest chain 16 peptides. Score 0.571 Taking the results from Round 4 Chains 43, Residues 280, Estimated correctness of the model 26.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9588 restraints for refining 4275 atoms. 8466 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2986 (Rfree = 0.000) for 4275 atoms. Found 32 (32 requested) and removed 79 (16 requested) atoms. Cycle 2: After refmac, R = 0.3011 (Rfree = 0.000) for 4160 atoms. Found 31 (31 requested) and removed 74 (15 requested) atoms. Cycle 3: After refmac, R = 0.2849 (Rfree = 0.000) for 4078 atoms. Found 31 (31 requested) and removed 52 (15 requested) atoms. Cycle 4: After refmac, R = 0.2821 (Rfree = 0.000) for 4021 atoms. Found 30 (30 requested) and removed 41 (15 requested) atoms. Cycle 5: After refmac, R = 0.2872 (Rfree = 0.000) for 3978 atoms. Found 30 (30 requested) and removed 42 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.49 Search for helices and strands: 0 residues in 0 chains, 4147 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4162 seeds are put forward Round 1: 244 peptides, 49 chains. Longest chain 8 peptides. Score 0.321 Round 2: 272 peptides, 48 chains. Longest chain 13 peptides. Score 0.414 Round 3: 297 peptides, 46 chains. Longest chain 17 peptides. Score 0.502 Round 4: 300 peptides, 43 chains. Longest chain 24 peptides. Score 0.541 Round 5: 302 peptides, 42 chains. Longest chain 17 peptides. Score 0.556 Taking the results from Round 5 Chains 44, Residues 260, Estimated correctness of the model 13.7 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 8789 restraints for refining 4096 atoms. 7699 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2608 (Rfree = 0.000) for 4096 atoms. Found 30 (30 requested) and removed 70 (15 requested) atoms. Cycle 7: After refmac, R = 0.2894 (Rfree = 0.000) for 4018 atoms. Found 30 (30 requested) and removed 56 (15 requested) atoms. Cycle 8: After refmac, R = 0.2444 (Rfree = 0.000) for 3952 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. Cycle 9: After refmac, R = 0.2285 (Rfree = 0.000) for 3936 atoms. Found 25 (29 requested) and removed 26 (14 requested) atoms. Cycle 10: After refmac, R = 0.2051 (Rfree = 0.000) for 3914 atoms. Found 18 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 4057 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4071 seeds are put forward Round 1: 261 peptides, 52 chains. Longest chain 10 peptides. Score 0.334 Round 2: 308 peptides, 53 chains. Longest chain 12 peptides. Score 0.454 Round 3: 312 peptides, 48 chains. Longest chain 16 peptides. Score 0.518 Round 4: 303 peptides, 48 chains. Longest chain 20 peptides. Score 0.496 Round 5: 319 peptides, 48 chains. Longest chain 19 peptides. Score 0.534 Taking the results from Round 5 Chains 48, Residues 271, Estimated correctness of the model 5.7 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9056 restraints for refining 4113 atoms. 7998 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2518 (Rfree = 0.000) for 4113 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 12: After refmac, R = 0.2510 (Rfree = 0.000) for 4051 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 13: After refmac, R = 0.2433 (Rfree = 0.000) for 4009 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. Cycle 14: After refmac, R = 0.2261 (Rfree = 0.000) for 3986 atoms. Found 30 (30 requested) and removed 20 (15 requested) atoms. Cycle 15: After refmac, R = 0.2324 (Rfree = 0.000) for 3976 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.50 Search for helices and strands: 0 residues in 0 chains, 4105 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4125 seeds are put forward Round 1: 224 peptides, 45 chains. Longest chain 10 peptides. Score 0.311 Round 2: 256 peptides, 43 chains. Longest chain 14 peptides. Score 0.429 Round 3: 253 peptides, 40 chains. Longest chain 16 peptides. Score 0.456 Round 4: 263 peptides, 43 chains. Longest chain 14 peptides. Score 0.448 Round 5: 257 peptides, 36 chains. Longest chain 17 peptides. Score 0.512 Taking the results from Round 5 Chains 36, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 8895 restraints for refining 4001 atoms. 8047 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2663 (Rfree = 0.000) for 4001 atoms. Found 30 (30 requested) and removed 56 (15 requested) atoms. Cycle 17: After refmac, R = 0.2330 (Rfree = 0.000) for 3945 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 18: After refmac, R = 0.2338 (Rfree = 0.000) for 3936 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 19: After refmac, R = 0.2419 (Rfree = 0.000) for 3924 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 20: After refmac, R = 0.2305 (Rfree = 0.000) for 3907 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.56 Search for helices and strands: 0 residues in 0 chains, 3989 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4010 seeds are put forward Round 1: 223 peptides, 45 chains. Longest chain 11 peptides. Score 0.308 Round 2: 264 peptides, 47 chains. Longest chain 14 peptides. Score 0.404 Round 3: 266 peptides, 45 chains. Longest chain 13 peptides. Score 0.433 Round 4: 259 peptides, 44 chains. Longest chain 18 peptides. Score 0.426 Round 5: 250 peptides, 40 chains. Longest chain 16 peptides. Score 0.448 Taking the results from Round 5 Chains 40, Residues 210, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 8958 restraints for refining 4036 atoms. 8139 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2487 (Rfree = 0.000) for 4036 atoms. Found 30 (30 requested) and removed 44 (15 requested) atoms. Cycle 22: After refmac, R = 0.2269 (Rfree = 0.000) for 4005 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Cycle 23: After refmac, R = 0.2291 (Rfree = 0.000) for 4000 atoms. Found 30 (30 requested) and removed 34 (15 requested) atoms. Cycle 24: After refmac, R = 0.1926 (Rfree = 0.000) for 3987 atoms. Found 15 (30 requested) and removed 21 (15 requested) atoms. Cycle 25: After refmac, R = 0.2034 (Rfree = 0.000) for 3963 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.50 Search for helices and strands: 0 residues in 0 chains, 4064 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4082 seeds are put forward Round 1: 214 peptides, 41 chains. Longest chain 10 peptides. Score 0.332 Round 2: 264 peptides, 48 chains. Longest chain 13 peptides. Score 0.392 Round 3: 274 peptides, 49 chains. Longest chain 13 peptides. Score 0.408 Round 4: 279 peptides, 46 chains. Longest chain 14 peptides. Score 0.456 Round 5: 266 peptides, 42 chains. Longest chain 13 peptides. Score 0.468 Taking the results from Round 5 Chains 42, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9209 restraints for refining 4111 atoms. 8355 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2307 (Rfree = 0.000) for 4111 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 27: After refmac, R = 0.2477 (Rfree = 0.000) for 4089 atoms. Found 31 (31 requested) and removed 44 (15 requested) atoms. Cycle 28: After refmac, R = 0.2167 (Rfree = 0.000) for 4051 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. Cycle 29: After refmac, R = 0.1815 (Rfree = 0.000) for 4046 atoms. Found 19 (30 requested) and removed 18 (15 requested) atoms. Cycle 30: After refmac, R = 0.1692 (Rfree = 0.000) for 4037 atoms. Found 9 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.47 Search for helices and strands: 0 residues in 0 chains, 4135 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4150 seeds are put forward Round 1: 218 peptides, 44 chains. Longest chain 9 peptides. Score 0.305 Round 2: 257 peptides, 43 chains. Longest chain 14 peptides. Score 0.432 Round 3: 246 peptides, 38 chains. Longest chain 14 peptides. Score 0.461 Round 4: 241 peptides, 38 chains. Longest chain 17 peptides. Score 0.448 Round 5: 237 peptides, 37 chains. Longest chain 17 peptides. Score 0.449 Taking the results from Round 3 Chains 39, Residues 208, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 8809 restraints for refining 4087 atoms. 7909 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2133 (Rfree = 0.000) for 4087 atoms. Found 30 (30 requested) and removed 34 (15 requested) atoms. Cycle 32: After refmac, R = 0.1971 (Rfree = 0.000) for 4069 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. Cycle 33: After refmac, R = 0.1841 (Rfree = 0.000) for 4065 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 34: After refmac, R = 0.1481 (Rfree = 0.000) for 4053 atoms. Found 9 (30 requested) and removed 17 (15 requested) atoms. Cycle 35: After refmac, R = 0.1591 (Rfree = 0.000) for 4040 atoms. Found 13 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.48 Search for helices and strands: 0 residues in 0 chains, 4151 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 4166 seeds are put forward Round 1: 207 peptides, 41 chains. Longest chain 10 peptides. Score 0.310 Round 2: 253 peptides, 42 chains. Longest chain 15 peptides. Score 0.433 Round 3: 252 peptides, 44 chains. Longest chain 14 peptides. Score 0.406 Round 4: 244 peptides, 43 chains. Longest chain 13 peptides. Score 0.396 Round 5: 255 peptides, 42 chains. Longest chain 16 peptides. Score 0.438 Taking the results from Round 5 Chains 42, Residues 213, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9444 restraints for refining 4199 atoms. 8601 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2004 (Rfree = 0.000) for 4199 atoms. Found 30 (31 requested) and removed 51 (15 requested) atoms. Cycle 37: After refmac, R = 0.1822 (Rfree = 0.000) for 4159 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. Cycle 38: After refmac, R = 0.1731 (Rfree = 0.000) for 4164 atoms. Found 30 (31 requested) and removed 21 (15 requested) atoms. Cycle 39: After refmac, R = 0.1669 (Rfree = 0.000) for 4165 atoms. Found 26 (31 requested) and removed 19 (15 requested) atoms. Cycle 40: After refmac, R = 0.1648 (Rfree = 0.000) for 4162 atoms. Found 23 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.48 Search for helices and strands: 0 residues in 0 chains, 4279 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4303 seeds are put forward Round 1: 187 peptides, 39 chains. Longest chain 12 peptides. Score 0.273 Round 2: 217 peptides, 40 chains. Longest chain 12 peptides. Score 0.354 Round 3: 232 peptides, 42 chains. Longest chain 12 peptides. Score 0.373 Round 4: 254 peptides, 45 chains. Longest chain 12 peptides. Score 0.400 Round 5: 249 peptides, 44 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 4 Chains 45, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9810 restraints for refining 4269 atoms. 9019 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1906 (Rfree = 0.000) for 4269 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 42: After refmac, R = 0.2045 (Rfree = 0.000) for 4257 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 43: After refmac, R = 0.1938 (Rfree = 0.000) for 4244 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 44: After refmac, R = 0.1993 (Rfree = 0.000) for 4241 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 45: After refmac, R = 0.1556 (Rfree = 0.000) for 4234 atoms. Found 21 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.50 Search for helices and strands: 0 residues in 0 chains, 4359 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4372 seeds are put forward Round 1: 177 peptides, 38 chains. Longest chain 9 peptides. Score 0.254 Round 2: 221 peptides, 44 chains. Longest chain 10 peptides. Score 0.315 Round 3: 221 peptides, 40 chains. Longest chain 11 peptides. Score 0.366 Round 4: 220 peptides, 39 chains. Longest chain 12 peptides. Score 0.376 Round 5: 208 peptides, 37 chains. Longest chain 12 peptides. Score 0.366 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 181, 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 2f4p-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7529 reflections ( 99.56 % complete ) and 9996 restraints for refining 4243 atoms. 9311 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2323 (Rfree = 0.000) for 4243 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1895 (Rfree = 0.000) for 4213 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1689 (Rfree = 0.000) for 4188 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1550 (Rfree = 0.000) for 4170 atoms. TimeTaking 65.87