null Sun 23 Dec 22:23:10 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.6-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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.6-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 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-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-3.6-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 3.600 Wilson plot Bfac: 72.38 7478 reflections ( 99.45 % complete ) and 0 restraints for refining 5147 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3617 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3335 (Rfree = 0.000) for 5147 atoms. Found 33 (33 requested) and removed 67 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 5208 seeds are put forward NCS extension: 0 residues added, 5208 seeds are put forward Round 1: 226 peptides, 47 chains. Longest chain 9 peptides. Score 0.284 Round 2: 268 peptides, 45 chains. Longest chain 13 peptides. Score 0.424 Round 3: 277 peptides, 44 chains. Longest chain 14 peptides. Score 0.457 Round 4: 299 peptides, 48 chains. Longest chain 13 peptides. Score 0.469 Round 5: 295 peptides, 46 chains. Longest chain 12 peptides. Score 0.480 Taking the results from Round 5 Chains 46, Residues 249, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9805 restraints for refining 4199 atoms. 8855 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2563 (Rfree = 0.000) for 4199 atoms. Found 16 (26 requested) and removed 23 (13 requested) atoms. Cycle 2: After refmac, R = 0.2415 (Rfree = 0.000) for 4136 atoms. Found 15 (26 requested) and removed 23 (13 requested) atoms. Cycle 3: After refmac, R = 0.2294 (Rfree = 0.000) for 4098 atoms. Found 17 (26 requested) and removed 23 (13 requested) atoms. Cycle 4: After refmac, R = 0.2277 (Rfree = 0.000) for 4067 atoms. Found 17 (26 requested) and removed 19 (13 requested) atoms. Cycle 5: After refmac, R = 0.2147 (Rfree = 0.000) for 4053 atoms. Found 6 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 4235 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4247 seeds are put forward Round 1: 232 peptides, 43 chains. Longest chain 9 peptides. Score 0.350 Round 2: 250 peptides, 40 chains. Longest chain 13 peptides. Score 0.433 Round 3: 248 peptides, 38 chains. Longest chain 14 peptides. Score 0.450 Round 4: 225 peptides, 33 chains. Longest chain 12 peptides. Score 0.448 Round 5: 257 peptides, 36 chains. Longest chain 16 peptides. Score 0.494 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 ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9703 restraints for refining 4158 atoms. 8855 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2224 (Rfree = 0.000) for 4158 atoms. Found 15 (26 requested) and removed 22 (13 requested) atoms. Cycle 7: After refmac, R = 0.2124 (Rfree = 0.000) for 4134 atoms. Found 17 (26 requested) and removed 21 (13 requested) atoms. Cycle 8: After refmac, R = 0.2193 (Rfree = 0.000) for 4121 atoms. Found 22 (26 requested) and removed 18 (13 requested) atoms. Cycle 9: After refmac, R = 0.2090 (Rfree = 0.000) for 4118 atoms. Found 19 (26 requested) and removed 14 (13 requested) atoms. Cycle 10: After refmac, R = 0.2001 (Rfree = 0.000) for 4117 atoms. Found 19 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 4263 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4276 seeds are put forward Round 1: 223 peptides, 45 chains. Longest chain 11 peptides. Score 0.300 Round 2: 267 peptides, 43 chains. Longest chain 14 peptides. Score 0.443 Round 3: 287 peptides, 45 chains. Longest chain 12 peptides. Score 0.471 Round 4: 273 peptides, 42 chains. Longest chain 12 peptides. Score 0.469 Round 5: 271 peptides, 39 chains. Longest chain 15 peptides. Score 0.496 Taking the results from Round 5 Chains 39, Residues 232, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9543 restraints for refining 4199 atoms. 8620 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2587 (Rfree = 0.000) for 4199 atoms. Found 23 (26 requested) and removed 25 (13 requested) atoms. Cycle 12: After refmac, R = 0.2338 (Rfree = 0.000) for 4147 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. Cycle 13: After refmac, R = 0.2348 (Rfree = 0.000) for 4127 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. Cycle 14: After refmac, R = 0.2237 (Rfree = 0.000) for 4110 atoms. Found 24 (26 requested) and removed 19 (13 requested) atoms. Cycle 15: After refmac, R = 0.1798 (Rfree = 0.000) for 4096 atoms. Found 6 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 4258 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4270 seeds are put forward Round 1: 200 peptides, 40 chains. Longest chain 9 peptides. Score 0.294 Round 2: 240 peptides, 44 chains. Longest chain 9 peptides. Score 0.360 Round 3: 253 peptides, 43 chains. Longest chain 10 peptides. Score 0.407 Round 4: 276 peptides, 46 chains. Longest chain 12 peptides. Score 0.433 Round 5: 281 peptides, 43 chains. Longest chain 19 peptides. Score 0.478 Taking the results from Round 5 Chains 43, Residues 238, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9300 restraints for refining 4135 atoms. 8391 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2480 (Rfree = 0.000) for 4135 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 17: After refmac, R = 0.2466 (Rfree = 0.000) for 4093 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 18: After refmac, R = 0.2379 (Rfree = 0.000) for 4064 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 19: After refmac, R = 0.2511 (Rfree = 0.000) for 4042 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 20: After refmac, R = 0.2383 (Rfree = 0.000) for 4033 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 4205 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 4242 seeds are put forward Round 1: 205 peptides, 43 chains. Longest chain 10 peptides. Score 0.271 Round 2: 247 peptides, 47 chains. Longest chain 12 peptides. Score 0.344 Round 3: 253 peptides, 43 chains. Longest chain 12 peptides. Score 0.407 Round 4: 270 peptides, 45 chains. Longest chain 19 peptides. Score 0.429 Round 5: 267 peptides, 45 chains. Longest chain 14 peptides. Score 0.421 Taking the results from Round 4 Chains 45, Residues 225, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9179 restraints for refining 4103 atoms. 8324 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2352 (Rfree = 0.000) for 4103 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. Cycle 22: After refmac, R = 0.2159 (Rfree = 0.000) for 4072 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 23: After refmac, R = 0.1947 (Rfree = 0.000) for 4063 atoms. Found 17 (26 requested) and removed 17 (13 requested) atoms. Cycle 24: After refmac, R = 0.2023 (Rfree = 0.000) for 4053 atoms. Found 24 (26 requested) and removed 19 (13 requested) atoms. Cycle 25: After refmac, R = 0.1916 (Rfree = 0.000) for 4054 atoms. Found 20 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 4190 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 4208 seeds are put forward Round 1: 208 peptides, 44 chains. Longest chain 9 peptides. Score 0.268 Round 2: 244 peptides, 44 chains. Longest chain 10 peptides. Score 0.371 Round 3: 236 peptides, 41 chains. Longest chain 11 peptides. Score 0.385 Round 4: 259 peptides, 45 chains. Longest chain 12 peptides. Score 0.400 Round 5: 267 peptides, 48 chains. Longest chain 12 peptides. Score 0.387 Taking the results from Round 4 Chains 45, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9658 restraints for refining 4198 atoms. 8847 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2253 (Rfree = 0.000) for 4198 atoms. Found 23 (26 requested) and removed 32 (13 requested) atoms. Cycle 27: After refmac, R = 0.2248 (Rfree = 0.000) for 4171 atoms. Found 26 (26 requested) and removed 26 (13 requested) atoms. Cycle 28: After refmac, R = 0.1857 (Rfree = 0.000) for 4155 atoms. Found 8 (26 requested) and removed 16 (13 requested) atoms. Cycle 29: After refmac, R = 0.1780 (Rfree = 0.000) for 4138 atoms. Found 6 (26 requested) and removed 18 (13 requested) atoms. Cycle 30: After refmac, R = 0.1747 (Rfree = 0.000) for 4120 atoms. Found 5 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 4211 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4227 seeds are put forward Round 1: 225 peptides, 47 chains. Longest chain 10 peptides. Score 0.281 Round 2: 237 peptides, 39 chains. Longest chain 15 peptides. Score 0.411 Round 3: 251 peptides, 43 chains. Longest chain 17 peptides. Score 0.402 Round 4: 264 peptides, 42 chains. Longest chain 16 peptides. Score 0.447 Round 5: 258 peptides, 43 chains. Longest chain 18 peptides. Score 0.420 Taking the results from Round 4 Chains 42, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9423 restraints for refining 4199 atoms. 8577 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2312 (Rfree = 0.000) for 4199 atoms. Found 22 (26 requested) and removed 29 (13 requested) atoms. Cycle 32: After refmac, R = 0.2290 (Rfree = 0.000) for 4169 atoms. Found 20 (26 requested) and removed 20 (13 requested) atoms. Cycle 33: After refmac, R = 0.2265 (Rfree = 0.000) for 4150 atoms. Found 21 (26 requested) and removed 21 (13 requested) atoms. Cycle 34: After refmac, R = 0.1828 (Rfree = 0.000) for 4142 atoms. Found 6 (26 requested) and removed 16 (13 requested) atoms. Cycle 35: After refmac, R = 0.1757 (Rfree = 0.000) for 4123 atoms. Found 5 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 4233 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4252 seeds are put forward Round 1: 197 peptides, 41 chains. Longest chain 9 peptides. Score 0.273 Round 2: 227 peptides, 43 chains. Longest chain 10 peptides. Score 0.336 Round 3: 247 peptides, 45 chains. Longest chain 9 peptides. Score 0.368 Round 4: 233 peptides, 35 chains. Longest chain 14 peptides. Score 0.446 Round 5: 230 peptides, 39 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 4 Chains 35, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9609 restraints for refining 4199 atoms. 8852 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2365 (Rfree = 0.000) for 4199 atoms. Found 26 (26 requested) and removed 33 (13 requested) atoms. Cycle 37: After refmac, R = 0.2342 (Rfree = 0.000) for 4181 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 38: After refmac, R = 0.2234 (Rfree = 0.000) for 4173 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 39: After refmac, R = 0.2237 (Rfree = 0.000) for 4163 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 40: After refmac, R = 0.1837 (Rfree = 0.000) for 4167 atoms. Found 8 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 4287 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4299 seeds are put forward Round 1: 186 peptides, 40 chains. Longest chain 8 peptides. Score 0.252 Round 2: 228 peptides, 42 chains. Longest chain 11 peptides. Score 0.351 Round 3: 213 peptides, 38 chains. Longest chain 12 peptides. Score 0.357 Round 4: 215 peptides, 36 chains. Longest chain 12 peptides. Score 0.387 Round 5: 198 peptides, 34 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 4 Chains 36, Residues 179, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7478 reflections ( 99.45 % complete ) and 9864 restraints for refining 4199 atoms. 9157 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2090 (Rfree = 0.000) for 4199 atoms. Found 21 (26 requested) and removed 23 (13 requested) atoms. Cycle 42: After refmac, R = 0.1994 (Rfree = 0.000) for 4177 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 43: After refmac, R = 0.1823 (Rfree = 0.000) for 4172 atoms. Found 12 (26 requested) and removed 19 (13 requested) atoms. Cycle 44: After refmac, R = 0.1929 (Rfree = 0.000) for 4160 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. Cycle 45: After refmac, R = 0.1877 (Rfree = 0.000) for 4163 atoms. Found 19 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.57 Search for helices and strands: 0 residues in 0 chains, 4290 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4303 seeds are put forward Round 1: 167 peptides, 38 chains. Longest chain 6 peptides. Score 0.217 Round 2: 192 peptides, 36 chains. Longest chain 9 peptides. Score 0.321 Round 3: 194 peptides, 36 chains. Longest chain 10 peptides. Score 0.327 Round 4: 210 peptides, 35 chains. Longest chain 12 peptides. Score 0.385 Round 5: 203 peptides, 33 chains. Longest chain 14 peptides. Score 0.390 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 170, Estimated correctness of the model 0.0 % 1 chains (6 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. 7478 reflections ( 99.45 % complete ) and 9702 restraints for refining 4199 atoms. 9035 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1948 (Rfree = 0.000) for 4199 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1999 (Rfree = 0.000) for 4171 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1940 (Rfree = 0.000) for 4149 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1920 (Rfree = 0.000) for 4125 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:25:41 GMT 2018 Job finished. TimeTaking 62.52 Used memory is bytes: 16036672