Sun 23 Dec 22:23:01 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 1z82-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z82-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z82-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-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/1z82-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-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 22:23:11 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/1z82-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-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 380 and 0 Target number of residues in the AU: 380 Target solvent content: 0.6624 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-4.0-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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5360 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: 29.850 4.002 Wilson plot Bfac: 86.40 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 5179 reflections ( 99.50 % complete ) and 0 restraints for refining 5967 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3219 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3054 (Rfree = 0.000) for 5967 atoms. Found 28 (28 requested) and removed 50 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 4.19 Search for helices and strands: 0 residues in 0 chains, 6074 seeds are put forward NCS extension: 0 residues added, 6074 seeds are put forward Round 1: 145 peptides, 33 chains. Longest chain 7 peptides. Score 0.212 Round 2: 186 peptides, 38 chains. Longest chain 10 peptides. Score 0.277 Round 3: 221 peptides, 44 chains. Longest chain 10 peptides. Score 0.306 Round 4: 234 peptides, 45 chains. Longest chain 9 peptides. Score 0.331 Round 5: 252 peptides, 48 chains. Longest chain 10 peptides. Score 0.346 Taking the results from Round 5 Chains 48, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 12004 restraints for refining 4840 atoms. 11236 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2501 (Rfree = 0.000) for 4840 atoms. Found 19 (22 requested) and removed 35 (11 requested) atoms. Cycle 2: After refmac, R = 0.2341 (Rfree = 0.000) for 4730 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. Cycle 3: After refmac, R = 0.2406 (Rfree = 0.000) for 4668 atoms. Found 21 (22 requested) and removed 24 (11 requested) atoms. Cycle 4: After refmac, R = 0.2438 (Rfree = 0.000) for 4624 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 5: After refmac, R = 0.1823 (Rfree = 0.000) for 4569 atoms. Found 7 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 4.35 Search for helices and strands: 0 residues in 0 chains, 4719 seeds are put forward NCS extension: 0 residues added, 4719 seeds are put forward Round 1: 176 peptides, 39 chains. Longest chain 10 peptides. Score 0.233 Round 2: 232 peptides, 45 chains. Longest chain 11 peptides. Score 0.325 Round 3: 236 peptides, 42 chains. Longest chain 12 peptides. Score 0.372 Round 4: 261 peptides, 45 chains. Longest chain 15 peptides. Score 0.404 Round 5: 273 peptides, 47 chains. Longest chain 13 peptides. Score 0.413 Taking the results from Round 5 Chains 47, Residues 226, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9711 restraints for refining 4193 atoms. 8828 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2190 (Rfree = 0.000) for 4193 atoms. Found 19 (19 requested) and removed 41 (9 requested) atoms. Cycle 7: After refmac, R = 0.2065 (Rfree = 0.000) for 4132 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 8: After refmac, R = 0.2175 (Rfree = 0.000) for 4096 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 9: After refmac, R = 0.1938 (Rfree = 0.000) for 4069 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 10: After refmac, R = 0.1890 (Rfree = 0.000) for 4055 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 4.31 Search for helices and strands: 0 residues in 0 chains, 4238 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4255 seeds are put forward Round 1: 207 peptides, 42 chains. Longest chain 10 peptides. Score 0.289 Round 2: 237 peptides, 41 chains. Longest chain 10 peptides. Score 0.386 Round 3: 252 peptides, 44 chains. Longest chain 10 peptides. Score 0.392 Round 4: 266 peptides, 40 chains. Longest chain 14 peptides. Score 0.472 Round 5: 265 peptides, 40 chains. Longest chain 12 peptides. Score 0.469 Taking the results from Round 4 Chains 41, Residues 226, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9272 restraints for refining 4131 atoms. 8372 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2143 (Rfree = 0.000) for 4131 atoms. Found 19 (19 requested) and removed 40 (9 requested) atoms. Cycle 12: After refmac, R = 0.2050 (Rfree = 0.000) for 4080 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 13: After refmac, R = 0.2067 (Rfree = 0.000) for 4051 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 14: After refmac, R = 0.2040 (Rfree = 0.000) for 4035 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 15: After refmac, R = 0.1912 (Rfree = 0.000) for 4017 atoms. Found 13 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 4.26 Search for helices and strands: 0 residues in 0 chains, 4199 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4214 seeds are put forward Round 1: 214 peptides, 42 chains. Longest chain 10 peptides. Score 0.310 Round 2: 265 peptides, 47 chains. Longest chain 12 peptides. Score 0.392 Round 3: 264 peptides, 42 chains. Longest chain 19 peptides. Score 0.445 Round 4: 245 peptides, 42 chains. Longest chain 15 peptides. Score 0.396 Round 5: 250 peptides, 41 chains. Longest chain 14 peptides. Score 0.421 Taking the results from Round 3 Chains 43, Residues 222, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9383 restraints for refining 4170 atoms. 8490 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2045 (Rfree = 0.000) for 4170 atoms. Found 19 (19 requested) and removed 39 (9 requested) atoms. Cycle 17: After refmac, R = 0.2045 (Rfree = 0.000) for 4130 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 18: After refmac, R = 0.2067 (Rfree = 0.000) for 4106 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 19: After refmac, R = 0.1996 (Rfree = 0.000) for 4083 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 20: After refmac, R = 0.1554 (Rfree = 0.000) for 4069 atoms. Found 4 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 4.35 Search for helices and strands: 0 residues in 0 chains, 4229 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 4239 seeds are put forward Round 1: 215 peptides, 44 chains. Longest chain 9 peptides. Score 0.288 Round 2: 257 peptides, 46 chains. Longest chain 10 peptides. Score 0.382 Round 3: 269 peptides, 48 chains. Longest chain 10 peptides. Score 0.391 Round 4: 262 peptides, 44 chains. Longest chain 10 peptides. Score 0.418 Round 5: 250 peptides, 43 chains. Longest chain 12 peptides. Score 0.398 Taking the results from Round 4 Chains 44, Residues 218, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9460 restraints for refining 4122 atoms. 8620 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2023 (Rfree = 0.000) for 4122 atoms. Found 19 (19 requested) and removed 35 (9 requested) atoms. Cycle 22: After refmac, R = 0.2293 (Rfree = 0.000) for 4088 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 23: After refmac, R = 0.1978 (Rfree = 0.000) for 4062 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 24: After refmac, R = 0.1614 (Rfree = 0.000) for 4049 atoms. Found 11 (19 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.1531 (Rfree = 0.000) for 4042 atoms. Found 3 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 4.33 Search for helices and strands: 0 residues in 0 chains, 4196 seeds are put forward NCS extension: 0 residues added, 4196 seeds are put forward Round 1: 193 peptides, 43 chains. Longest chain 6 peptides. Score 0.234 Round 2: 239 peptides, 44 chains. Longest chain 19 peptides. Score 0.357 Round 3: 244 peptides, 43 chains. Longest chain 19 peptides. Score 0.382 Round 4: 233 peptides, 38 chains. Longest chain 20 peptides. Score 0.410 Round 5: 252 peptides, 43 chains. Longest chain 12 peptides. Score 0.403 Taking the results from Round 4 Chains 38, Residues 195, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9424 restraints for refining 4164 atoms. 8612 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2124 (Rfree = 0.000) for 4164 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 27: After refmac, R = 0.2096 (Rfree = 0.000) for 4130 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 28: After refmac, R = 0.2084 (Rfree = 0.000) for 4106 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 29: After refmac, R = 0.1987 (Rfree = 0.000) for 4086 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 30: After refmac, R = 0.1889 (Rfree = 0.000) for 4079 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 4.30 Search for helices and strands: 0 residues in 0 chains, 4223 seeds are put forward NCS extension: 38 residues added (0 deleted due to clashes), 4261 seeds are put forward Round 1: 217 peptides, 42 chains. Longest chain 10 peptides. Score 0.319 Round 2: 217 peptides, 38 chains. Longest chain 13 peptides. Score 0.367 Round 3: 210 peptides, 32 chains. Longest chain 11 peptides. Score 0.420 Round 4: 211 peptides, 34 chains. Longest chain 17 peptides. Score 0.399 Round 5: 210 peptides, 34 chains. Longest chain 15 peptides. Score 0.396 Taking the results from Round 3 Chains 32, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9687 restraints for refining 4132 atoms. 9007 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2170 (Rfree = 0.000) for 4132 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 32: After refmac, R = 0.1950 (Rfree = 0.000) for 4092 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 33: After refmac, R = 0.1851 (Rfree = 0.000) for 4071 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 34: After refmac, R = 0.1885 (Rfree = 0.000) for 4063 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 35: After refmac, R = 0.1684 (Rfree = 0.000) for 4051 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 4.26 Search for helices and strands: 0 residues in 0 chains, 4191 seeds are put forward NCS extension: 4 residues added (2 deleted due to clashes), 4195 seeds are put forward Round 1: 176 peptides, 40 chains. Longest chain 7 peptides. Score 0.220 Round 2: 206 peptides, 42 chains. Longest chain 8 peptides. Score 0.286 Round 3: 199 peptides, 36 chains. Longest chain 9 peptides. Score 0.341 Round 4: 199 peptides, 37 chains. Longest chain 8 peptides. Score 0.328 Round 5: 212 peptides, 36 chains. Longest chain 16 peptides. Score 0.377 Taking the results from Round 5 Chains 36, Residues 176, Estimated correctness of the model 0.0 % 5 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9461 restraints for refining 4107 atoms. 8735 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2036 (Rfree = 0.000) for 4107 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 37: After refmac, R = 0.2044 (Rfree = 0.000) for 4074 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 38: After refmac, R = 0.1816 (Rfree = 0.000) for 4062 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 39: After refmac, R = 0.1551 (Rfree = 0.000) for 4053 atoms. Found 14 (19 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.1346 (Rfree = 0.000) for 4051 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 4.34 Search for helices and strands: 0 residues in 0 chains, 4186 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4202 seeds are put forward Round 1: 186 peptides, 39 chains. Longest chain 9 peptides. Score 0.264 Round 2: 203 peptides, 35 chains. Longest chain 11 peptides. Score 0.364 Round 3: 192 peptides, 32 chains. Longest chain 12 peptides. Score 0.370 Round 4: 191 peptides, 31 chains. Longest chain 11 peptides. Score 0.380 Round 5: 192 peptides, 33 chains. Longest chain 9 peptides. Score 0.358 Taking the results from Round 4 Chains 31, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9667 restraints for refining 4134 atoms. 9058 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2056 (Rfree = 0.000) for 4134 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 42: After refmac, R = 0.2183 (Rfree = 0.000) for 4109 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 43: After refmac, R = 0.1905 (Rfree = 0.000) for 4080 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 44: After refmac, R = 0.1502 (Rfree = 0.000) for 4066 atoms. Found 8 (19 requested) and removed 20 (9 requested) atoms. Cycle 45: After refmac, R = 0.1383 (Rfree = 0.000) for 4044 atoms. Found 4 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 4.30 Search for helices and strands: 0 residues in 0 chains, 4162 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4177 seeds are put forward Round 1: 146 peptides, 32 chains. Longest chain 9 peptides. Score 0.230 Round 2: 166 peptides, 32 chains. Longest chain 10 peptides. Score 0.294 Round 3: 159 peptides, 31 chains. Longest chain 8 peptides. Score 0.285 Round 4: 163 peptides, 31 chains. Longest chain 9 peptides. Score 0.298 Round 5: 176 peptides, 29 chains. Longest chain 15 peptides. Score 0.363 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 147, 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 1z82-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5179 reflections ( 99.50 % complete ) and 9488 restraints for refining 4075 atoms. 8929 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1919 (Rfree = 0.000) for 4075 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2092 (Rfree = 0.000) for 4058 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1743 (Rfree = 0.000) for 4036 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1938 (Rfree = 0.000) for 4013 atoms. TimeTaking 62.85