null Sun 23 Dec 22:22:56 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.8-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 22:23:05 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.8-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 391 and 0 Target number of residues in the AU: 391 Target solvent content: 0.6500 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-3.8-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-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4632 target number of atoms Had to go as low as 0.70 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 3.800 Wilson plot Bfac: 77.83 6403 reflections ( 99.39 % complete ) and 0 restraints for refining 5141 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3603 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3543 (Rfree = 0.000) for 5141 atoms. Found 28 (28 requested) and removed 165 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 5073 seeds are put forward NCS extension: 0 residues added, 5073 seeds are put forward Round 1: 127 peptides, 26 chains. Longest chain 12 peptides. Score 0.251 Round 2: 189 peptides, 35 chains. Longest chain 12 peptides. Score 0.325 Round 3: 217 peptides, 39 chains. Longest chain 12 peptides. Score 0.356 Round 4: 214 peptides, 38 chains. Longest chain 12 peptides. Score 0.360 Round 5: 227 peptides, 40 chains. Longest chain 11 peptides. Score 0.372 Taking the results from Round 5 Chains 40, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 10268 restraints for refining 4190 atoms. 9560 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2838 (Rfree = 0.000) for 4190 atoms. Found 23 (23 requested) and removed 44 (11 requested) atoms. Cycle 2: After refmac, R = 0.2631 (Rfree = 0.000) for 4118 atoms. Found 20 (22 requested) and removed 51 (11 requested) atoms. Cycle 3: After refmac, R = 0.2700 (Rfree = 0.000) for 4066 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 4: After refmac, R = 0.2139 (Rfree = 0.000) for 4034 atoms. Found 4 (22 requested) and removed 21 (11 requested) atoms. Cycle 5: After refmac, R = 0.2008 (Rfree = 0.000) for 4008 atoms. Found 6 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 4123 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4137 seeds are put forward Round 1: 204 peptides, 41 chains. Longest chain 8 peptides. Score 0.294 Round 2: 262 peptides, 48 chains. Longest chain 9 peptides. Score 0.374 Round 3: 267 peptides, 44 chains. Longest chain 11 peptides. Score 0.432 Round 4: 271 peptides, 43 chains. Longest chain 15 peptides. Score 0.453 Round 5: 264 peptides, 40 chains. Longest chain 17 peptides. Score 0.468 Taking the results from Round 5 Chains 40, Residues 224, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9825 restraints for refining 4189 atoms. 8943 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2449 (Rfree = 0.000) for 4189 atoms. Found 14 (23 requested) and removed 63 (11 requested) atoms. Cycle 7: After refmac, R = 0.2432 (Rfree = 0.000) for 4105 atoms. Found 21 (22 requested) and removed 30 (11 requested) atoms. Cycle 8: After refmac, R = 0.2312 (Rfree = 0.000) for 4073 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 9: After refmac, R = 0.2417 (Rfree = 0.000) for 4054 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 10: After refmac, R = 0.2282 (Rfree = 0.000) for 4028 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 4158 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 4178 seeds are put forward Round 1: 218 peptides, 44 chains. Longest chain 9 peptides. Score 0.298 Round 2: 241 peptides, 40 chains. Longest chain 14 peptides. Score 0.410 Round 3: 245 peptides, 39 chains. Longest chain 13 peptides. Score 0.432 Round 4: 241 peptides, 38 chains. Longest chain 13 peptides. Score 0.433 Round 5: 236 peptides, 35 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 5 Chains 35, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9696 restraints for refining 4143 atoms. 8927 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2438 (Rfree = 0.000) for 4143 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 12: After refmac, R = 0.2271 (Rfree = 0.000) for 4116 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 13: After refmac, R = 0.2345 (Rfree = 0.000) for 4107 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 14: After refmac, R = 0.2140 (Rfree = 0.000) for 4093 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 15: After refmac, R = 0.2148 (Rfree = 0.000) for 4086 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 4231 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4246 seeds are put forward Round 1: 210 peptides, 43 chains. Longest chain 8 peptides. Score 0.286 Round 2: 223 peptides, 42 chains. Longest chain 10 peptides. Score 0.337 Round 3: 235 peptides, 42 chains. Longest chain 11 peptides. Score 0.370 Round 4: 230 peptides, 39 chains. Longest chain 17 peptides. Score 0.392 Round 5: 224 peptides, 41 chains. Longest chain 10 peptides. Score 0.351 Taking the results from Round 4 Chains 39, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9720 restraints for refining 4190 atoms. 8995 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2150 (Rfree = 0.000) for 4190 atoms. Found 23 (23 requested) and removed 42 (11 requested) atoms. Cycle 17: After refmac, R = 0.2046 (Rfree = 0.000) for 4152 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 18: After refmac, R = 0.1958 (Rfree = 0.000) for 4131 atoms. Found 21 (22 requested) and removed 17 (11 requested) atoms. Cycle 19: After refmac, R = 0.2005 (Rfree = 0.000) for 4121 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 20: After refmac, R = 0.1967 (Rfree = 0.000) for 4105 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.59 Search for helices and strands: 0 residues in 0 chains, 4238 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4260 seeds are put forward Round 1: 191 peptides, 41 chains. Longest chain 8 peptides. Score 0.254 Round 2: 238 peptides, 44 chains. Longest chain 11 peptides. Score 0.355 Round 3: 246 peptides, 45 chains. Longest chain 15 peptides. Score 0.365 Round 4: 237 peptides, 42 chains. Longest chain 15 peptides. Score 0.376 Round 5: 246 peptides, 42 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 5 Chains 42, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9726 restraints for refining 4186 atoms. 8952 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2041 (Rfree = 0.000) for 4186 atoms. Found 8 (23 requested) and removed 22 (11 requested) atoms. Cycle 22: After refmac, R = 0.1890 (Rfree = 0.000) for 4155 atoms. Found 12 (22 requested) and removed 17 (11 requested) atoms. Cycle 23: After refmac, R = 0.1843 (Rfree = 0.000) for 4141 atoms. Found 11 (22 requested) and removed 18 (11 requested) atoms. Cycle 24: After refmac, R = 0.1729 (Rfree = 0.000) for 4124 atoms. Found 9 (22 requested) and removed 16 (11 requested) atoms. Cycle 25: After refmac, R = 0.1735 (Rfree = 0.000) for 4108 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 4243 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4256 seeds are put forward Round 1: 207 peptides, 39 chains. Longest chain 13 peptides. Score 0.327 Round 2: 230 peptides, 42 chains. Longest chain 15 peptides. Score 0.356 Round 3: 248 peptides, 42 chains. Longest chain 15 peptides. Score 0.405 Round 4: 259 peptides, 43 chains. Longest chain 14 peptides. Score 0.423 Round 5: 271 peptides, 43 chains. Longest chain 15 peptides. Score 0.453 Taking the results from Round 5 Chains 43, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9478 restraints for refining 4189 atoms. 8609 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2035 (Rfree = 0.000) for 4189 atoms. Found 17 (23 requested) and removed 30 (11 requested) atoms. Cycle 27: After refmac, R = 0.1923 (Rfree = 0.000) for 4158 atoms. Found 9 (22 requested) and removed 20 (11 requested) atoms. Cycle 28: After refmac, R = 0.1842 (Rfree = 0.000) for 4141 atoms. Found 2 (22 requested) and removed 16 (11 requested) atoms. Cycle 29: After refmac, R = 0.1830 (Rfree = 0.000) for 4121 atoms. Found 5 (22 requested) and removed 16 (11 requested) atoms. Cycle 30: After refmac, R = 0.1739 (Rfree = 0.000) for 4105 atoms. Found 2 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 4217 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4233 seeds are put forward Round 1: 217 peptides, 44 chains. Longest chain 10 peptides. Score 0.295 Round 2: 238 peptides, 39 chains. Longest chain 12 peptides. Score 0.413 Round 3: 241 peptides, 37 chains. Longest chain 14 peptides. Score 0.444 Round 4: 241 peptides, 37 chains. Longest chain 12 peptides. Score 0.444 Round 5: 234 peptides, 37 chains. Longest chain 13 peptides. Score 0.426 Taking the results from Round 4 Chains 37, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9553 restraints for refining 4190 atoms. 8774 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1940 (Rfree = 0.000) for 4190 atoms. Found 19 (23 requested) and removed 17 (11 requested) atoms. Cycle 32: After refmac, R = 0.1833 (Rfree = 0.000) for 4177 atoms. Found 6 (23 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.1801 (Rfree = 0.000) for 4164 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1868 (Rfree = 0.000) for 4151 atoms. Found 4 (22 requested) and removed 13 (11 requested) atoms. Cycle 35: After refmac, R = 0.1964 (Rfree = 0.000) for 4133 atoms. Found 12 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 4247 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4265 seeds are put forward Round 1: 204 peptides, 43 chains. Longest chain 10 peptides. Score 0.268 Round 2: 229 peptides, 40 chains. Longest chain 15 peptides. Score 0.377 Round 3: 246 peptides, 44 chains. Longest chain 12 peptides. Score 0.377 Round 4: 229 peptides, 40 chains. Longest chain 13 peptides. Score 0.377 Round 5: 232 peptides, 38 chains. Longest chain 19 peptides. Score 0.409 Taking the results from Round 5 Chains 38, Residues 194, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9623 restraints for refining 4190 atoms. 8853 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2037 (Rfree = 0.000) for 4190 atoms. Found 22 (23 requested) and removed 16 (11 requested) atoms. Cycle 37: After refmac, R = 0.1932 (Rfree = 0.000) for 4178 atoms. Found 19 (23 requested) and removed 16 (11 requested) atoms. Cycle 38: After refmac, R = 0.1542 (Rfree = 0.000) for 4170 atoms. Found 4 (22 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.1507 (Rfree = 0.000) for 4159 atoms. Found 0 (22 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1450 (Rfree = 0.000) for 4144 atoms. Found 0 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 4227 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4247 seeds are put forward Round 1: 163 peptides, 33 chains. Longest chain 9 peptides. Score 0.272 Round 2: 176 peptides, 35 chains. Longest chain 12 peptides. Score 0.286 Round 3: 182 peptides, 35 chains. Longest chain 11 peptides. Score 0.304 Round 4: 188 peptides, 35 chains. Longest chain 12 peptides. Score 0.322 Round 5: 183 peptides, 33 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 5 Chains 33, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 10068 restraints for refining 4190 atoms. 9501 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1871 (Rfree = 0.000) for 4190 atoms. Found 19 (23 requested) and removed 14 (11 requested) atoms. Cycle 42: After refmac, R = 0.1898 (Rfree = 0.000) for 4191 atoms. Found 23 (23 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.1990 (Rfree = 0.000) for 4195 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 44: After refmac, R = 0.1950 (Rfree = 0.000) for 4200 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 45: After refmac, R = 0.1904 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 4323 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 4325 seeds are put forward Round 1: 158 peptides, 33 chains. Longest chain 7 peptides. Score 0.256 Round 2: 192 peptides, 34 chains. Longest chain 10 peptides. Score 0.346 Round 3: 187 peptides, 30 chains. Longest chain 14 peptides. Score 0.382 Round 4: 197 peptides, 32 chains. Longest chain 15 peptides. Score 0.386 Round 5: 196 peptides, 30 chains. Longest chain 16 peptides. Score 0.407 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 166, 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. 6403 reflections ( 99.39 % complete ) and 9782 restraints for refining 4190 atoms. 9148 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1982 (Rfree = 0.000) for 4190 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2070 (Rfree = 0.000) for 4156 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2075 (Rfree = 0.000) for 4133 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1691 (Rfree = 0.000) for 4114 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:24:19 GMT 2018 Job finished. TimeTaking 61.38 Used memory is bytes: 824960