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 2gb5-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-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/2gb5-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-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/2gb5-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-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 394 and 0 Target number of residues in the AU: 394 Target solvent content: 0.6379 Checking the provided sequence file Detected sequence length: 269 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 538 Adjusted target solvent content: 0.51 Input MTZ file: 2gb5-3.6-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: 18 Cell parameters: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4304 target number of atoms Had to go as low as 0.80 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: 49.644 3.600 Wilson plot Bfac: 70.46 7206 reflections ( 99.41 % complete ) and 0 restraints for refining 4760 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3299 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3236 (Rfree = 0.000) for 4760 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 4828 seeds are put forward NCS extension: 0 residues added, 4828 seeds are put forward Round 1: 213 peptides, 43 chains. Longest chain 9 peptides. Score 0.298 Round 2: 262 peptides, 46 chains. Longest chain 18 peptides. Score 0.401 Round 3: 289 peptides, 42 chains. Longest chain 24 peptides. Score 0.513 Round 4: 297 peptides, 45 chains. Longest chain 15 peptides. Score 0.501 Round 5: 285 peptides, 39 chains. Longest chain 19 peptides. Score 0.535 Taking the results from Round 5 Chains 39, Residues 246, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9059 restraints for refining 3901 atoms. 8114 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2634 (Rfree = 0.000) for 3901 atoms. Found 12 (25 requested) and removed 18 (12 requested) atoms. Cycle 2: After refmac, R = 0.2597 (Rfree = 0.000) for 3822 atoms. Found 8 (24 requested) and removed 22 (12 requested) atoms. Cycle 3: After refmac, R = 0.2550 (Rfree = 0.000) for 3763 atoms. Found 15 (24 requested) and removed 15 (12 requested) atoms. Cycle 4: After refmac, R = 0.2666 (Rfree = 0.000) for 3743 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 5: After refmac, R = 0.2256 (Rfree = 0.000) for 3716 atoms. Found 9 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 3813 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3834 seeds are put forward Round 1: 241 peptides, 45 chains. Longest chain 13 peptides. Score 0.355 Round 2: 289 peptides, 42 chains. Longest chain 20 peptides. Score 0.513 Round 3: 292 peptides, 39 chains. Longest chain 22 peptides. Score 0.550 Round 4: 295 peptides, 40 chains. Longest chain 21 peptides. Score 0.547 Round 5: 294 peptides, 42 chains. Longest chain 22 peptides. Score 0.525 Taking the results from Round 3 Chains 39, Residues 253, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8237 restraints for refining 3695 atoms. 7216 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2448 (Rfree = 0.000) for 3695 atoms. Found 20 (23 requested) and removed 21 (11 requested) atoms. Cycle 7: After refmac, R = 0.2398 (Rfree = 0.000) for 3669 atoms. Found 21 (23 requested) and removed 24 (11 requested) atoms. Cycle 8: After refmac, R = 0.2175 (Rfree = 0.000) for 3658 atoms. Found 13 (23 requested) and removed 14 (11 requested) atoms. Cycle 9: After refmac, R = 0.2184 (Rfree = 0.000) for 3648 atoms. Found 11 (23 requested) and removed 20 (11 requested) atoms. Cycle 10: After refmac, R = 0.2175 (Rfree = 0.000) for 3632 atoms. Found 11 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 3744 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3773 seeds are put forward Round 1: 247 peptides, 42 chains. Longest chain 13 peptides. Score 0.407 Round 2: 270 peptides, 41 chains. Longest chain 23 peptides. Score 0.478 Round 3: 290 peptides, 41 chains. Longest chain 15 peptides. Score 0.526 Round 4: 292 peptides, 42 chains. Longest chain 17 peptides. Score 0.520 Round 5: 294 peptides, 35 chains. Longest chain 24 peptides. Score 0.594 Taking the results from Round 5 Chains 37, Residues 259, Estimated correctness of the model 12.3 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8635 restraints for refining 3902 atoms. 7574 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2366 (Rfree = 0.000) for 3902 atoms. Found 15 (25 requested) and removed 22 (12 requested) atoms. Cycle 12: After refmac, R = 0.2287 (Rfree = 0.000) for 3864 atoms. Found 19 (24 requested) and removed 22 (12 requested) atoms. Cycle 13: After refmac, R = 0.2182 (Rfree = 0.000) for 3847 atoms. Found 8 (24 requested) and removed 21 (12 requested) atoms. Cycle 14: After refmac, R = 0.2102 (Rfree = 0.000) for 3828 atoms. Found 9 (24 requested) and removed 19 (12 requested) atoms. Cycle 15: After refmac, R = 0.2069 (Rfree = 0.000) for 3817 atoms. Found 3 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 3893 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3917 seeds are put forward Round 1: 272 peptides, 47 chains. Longest chain 18 peptides. Score 0.416 Round 2: 295 peptides, 42 chains. Longest chain 19 peptides. Score 0.527 Round 3: 293 peptides, 38 chains. Longest chain 18 peptides. Score 0.563 Round 4: 301 peptides, 42 chains. Longest chain 22 peptides. Score 0.541 Round 5: 287 peptides, 40 chains. Longest chain 18 peptides. Score 0.529 Taking the results from Round 3 Chains 40, Residues 255, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8586 restraints for refining 3901 atoms. 7471 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2379 (Rfree = 0.000) for 3901 atoms. Found 18 (25 requested) and removed 21 (12 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2221 (Rfree = 0.000) for 3881 atoms. Found 6 (25 requested) and removed 17 (12 requested) atoms. Cycle 18: After refmac, R = 0.2164 (Rfree = 0.000) for 3868 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.2133 (Rfree = 0.000) for 3860 atoms. Found 2 (24 requested) and removed 14 (12 requested) atoms. Cycle 20: After refmac, R = 0.2114 (Rfree = 0.000) for 3847 atoms. Found 1 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 3904 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3924 seeds are put forward Round 1: 266 peptides, 49 chains. Longest chain 13 peptides. Score 0.377 Round 2: 284 peptides, 45 chains. Longest chain 12 peptides. Score 0.469 Round 3: 301 peptides, 47 chains. Longest chain 17 peptides. Score 0.490 Round 4: 303 peptides, 43 chains. Longest chain 16 peptides. Score 0.535 Round 5: 317 peptides, 45 chains. Longest chain 21 peptides. Score 0.547 Taking the results from Round 5 Chains 45, Residues 272, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8687 restraints for refining 3901 atoms. 7622 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2473 (Rfree = 0.000) for 3901 atoms. Found 20 (25 requested) and removed 23 (12 requested) atoms. Cycle 22: After refmac, R = 0.2301 (Rfree = 0.000) for 3885 atoms. Found 7 (25 requested) and removed 16 (12 requested) atoms. Cycle 23: After refmac, R = 0.2267 (Rfree = 0.000) for 3872 atoms. Found 6 (24 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.2258 (Rfree = 0.000) for 3860 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.2236 (Rfree = 0.000) for 3853 atoms. Found 1 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 3903 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3924 seeds are put forward Round 1: 239 peptides, 46 chains. Longest chain 13 peptides. Score 0.337 Round 2: 257 peptides, 39 chains. Longest chain 17 peptides. Score 0.467 Round 3: 271 peptides, 39 chains. Longest chain 18 peptides. Score 0.502 Round 4: 270 peptides, 38 chains. Longest chain 19 peptides. Score 0.510 Round 5: 288 peptides, 43 chains. Longest chain 19 peptides. Score 0.500 Taking the results from Round 4 Chains 38, Residues 232, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8990 restraints for refining 3902 atoms. 8069 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2466 (Rfree = 0.000) for 3902 atoms. Found 20 (25 requested) and removed 13 (12 requested) atoms. Cycle 27: After refmac, R = 0.2461 (Rfree = 0.000) for 3898 atoms. Found 19 (25 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2375 (Rfree = 0.000) for 3898 atoms. Found 20 (25 requested) and removed 16 (12 requested) atoms. Cycle 29: After refmac, R = 0.2038 (Rfree = 0.000) for 3890 atoms. Found 1 (25 requested) and removed 15 (12 requested) atoms. Cycle 30: After refmac, R = 0.2104 (Rfree = 0.000) for 3874 atoms. Found 9 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 3945 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3970 seeds are put forward Round 1: 248 peptides, 47 chains. Longest chain 14 peptides. Score 0.351 Round 2: 271 peptides, 45 chains. Longest chain 17 peptides. Score 0.436 Round 3: 263 peptides, 46 chains. Longest chain 17 peptides. Score 0.404 Round 4: 261 peptides, 42 chains. Longest chain 19 peptides. Score 0.444 Round 5: 242 peptides, 42 chains. Longest chain 17 peptides. Score 0.393 Taking the results from Round 4 Chains 42, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9196 restraints for refining 3902 atoms. 8362 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2305 (Rfree = 0.000) for 3902 atoms. Found 15 (25 requested) and removed 14 (12 requested) atoms. Cycle 32: After refmac, R = 0.2194 (Rfree = 0.000) for 3889 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.2189 (Rfree = 0.000) for 3877 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.2176 (Rfree = 0.000) for 3868 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.2171 (Rfree = 0.000) for 3858 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 3916 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 3948 seeds are put forward Round 1: 239 peptides, 47 chains. Longest chain 13 peptides. Score 0.325 Round 2: 269 peptides, 45 chains. Longest chain 14 peptides. Score 0.431 Round 3: 256 peptides, 40 chains. Longest chain 20 peptides. Score 0.454 Round 4: 271 peptides, 45 chains. Longest chain 19 peptides. Score 0.436 Round 5: 255 peptides, 42 chains. Longest chain 13 peptides. Score 0.428 Taking the results from Round 3 Chains 40, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9126 restraints for refining 3902 atoms. 8302 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2363 (Rfree = 0.000) for 3902 atoms. Found 8 (25 requested) and removed 16 (12 requested) atoms. Cycle 37: After refmac, R = 0.2247 (Rfree = 0.000) for 3886 atoms. Found 4 (24 requested) and removed 15 (12 requested) atoms. Cycle 38: After refmac, R = 0.2209 (Rfree = 0.000) for 3868 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.2165 (Rfree = 0.000) for 3859 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2146 (Rfree = 0.000) for 3850 atoms. Found 3 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 3909 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 3948 seeds are put forward Round 1: 217 peptides, 40 chains. Longest chain 15 peptides. Score 0.347 Round 2: 235 peptides, 39 chains. Longest chain 21 peptides. Score 0.410 Round 3: 240 peptides, 37 chains. Longest chain 12 peptides. Score 0.446 Round 4: 239 peptides, 39 chains. Longest chain 15 peptides. Score 0.421 Round 5: 247 peptides, 37 chains. Longest chain 19 peptides. Score 0.464 Taking the results from Round 5 Chains 37, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9246 restraints for refining 3902 atoms. 8443 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2506 (Rfree = 0.000) for 3902 atoms. Found 15 (25 requested) and removed 17 (12 requested) atoms. Cycle 42: After refmac, R = 0.2592 (Rfree = 0.000) for 3889 atoms. Found 16 (25 requested) and removed 14 (12 requested) atoms. Cycle 43: After refmac, R = 0.2517 (Rfree = 0.000) for 3878 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 44: After refmac, R = 0.2122 (Rfree = 0.000) for 3874 atoms. Found 4 (24 requested) and removed 44 (12 requested) atoms. Cycle 45: After refmac, R = 0.2073 (Rfree = 0.000) for 3826 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 3895 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 3924 seeds are put forward Round 1: 153 peptides, 31 chains. Longest chain 8 peptides. Score 0.269 Round 2: 166 peptides, 28 chains. Longest chain 13 peptides. Score 0.351 Round 3: 186 peptides, 31 chains. Longest chain 17 peptides. Score 0.371 Round 4: 185 peptides, 27 chains. Longest chain 17 peptides. Score 0.419 Round 5: 176 peptides, 27 chains. Longest chain 17 peptides. Score 0.393 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 158, 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 2gb5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7206 reflections ( 99.41 % complete ) and 9284 restraints for refining 3858 atoms. 8679 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2428 (Rfree = 0.000) for 3858 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2518 (Rfree = 0.000) for 3833 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2115 (Rfree = 0.000) for 3809 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2121 (Rfree = 0.000) for 3792 atoms. TimeTaking 57.72