Starting phenix.real_space_refine on Sat Aug 23 16:29:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijq_35492/08_2025/8ijq_35492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijq_35492/08_2025/8ijq_35492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ijq_35492/08_2025/8ijq_35492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijq_35492/08_2025/8ijq_35492.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ijq_35492/08_2025/8ijq_35492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijq_35492/08_2025/8ijq_35492.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 8994 2.51 5 N 2130 2.21 5 O 2142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13380 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "B" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "C" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "D" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.20, per 1000 atoms: 0.24 Number of scatterers: 13380 At special positions: 0 Unit cell: (161.7, 122.1, 79.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 2142 8.00 N 2130 7.00 C 8994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 293 " distance=2.04 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 293 " distance=2.04 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 293 " distance=2.04 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 293 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 403.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 0 sheets defined 60.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 151 through 177 removed outlier: 4.325A pdb=" N VAL A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 221 removed outlier: 3.909A pdb=" N GLU A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 250 removed outlier: 3.805A pdb=" N CYS A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.972A pdb=" N VAL A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 345 through 370 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'B' and resid 150 through 175 removed outlier: 3.611A pdb=" N LEU B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 221 removed outlier: 3.637A pdb=" N MET B 203 " --> pdb=" O TRP B 199 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 removed outlier: 3.587A pdb=" N LEU B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 237 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.921A pdb=" N VAL B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 3.548A pdb=" N ILE B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 368 removed outlier: 3.576A pdb=" N VAL B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.431A pdb=" N SER B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'C' and resid 148 through 177 removed outlier: 3.846A pdb=" N THR C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 153 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 172 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 221 removed outlier: 3.736A pdb=" N MET C 203 " --> pdb=" O TRP C 199 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 250 removed outlier: 3.645A pdb=" N ARG C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 237 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.946A pdb=" N VAL C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 341 removed outlier: 3.566A pdb=" N ASN C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 370 removed outlier: 3.706A pdb=" N VAL C 349 " --> pdb=" O TYR C 345 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 355 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 3.738A pdb=" N GLN C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 375' Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.691A pdb=" N PHE C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 175 removed outlier: 3.646A pdb=" N LEU D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 160 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 203 through 221 Processing helix chain 'D' and resid 224 through 250 removed outlier: 3.915A pdb=" N LEU D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR D 250 " --> pdb=" O THR D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.895A pdb=" N HIS D 274 " --> pdb=" O TRP D 270 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 315 removed outlier: 3.893A pdb=" N VAL D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 341 removed outlier: 3.561A pdb=" N LEU D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 339 " --> pdb=" O ILE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 370 removed outlier: 3.726A pdb=" N VAL D 349 " --> pdb=" O TYR D 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 351 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 355 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.748A pdb=" N GLN D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 375' Processing helix chain 'D' and resid 385 through 390 Processing helix chain 'E' and resid 148 through 177 removed outlier: 3.957A pdb=" N THR E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 154 " --> pdb=" O TRP E 150 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE E 160 " --> pdb=" O CYS E 156 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 172 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU E 175 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL E 177 " --> pdb=" O VAL E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 221 removed outlier: 3.676A pdb=" N GLY E 208 " --> pdb=" O THR E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 250 removed outlier: 3.925A pdb=" N LEU E 228 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR E 250 " --> pdb=" O THR E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 281 removed outlier: 3.993A pdb=" N ARG E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.891A pdb=" N VAL E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 341 removed outlier: 3.711A pdb=" N LEU E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 370 removed outlier: 3.781A pdb=" N VAL E 349 " --> pdb=" O TYR E 345 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 390 removed outlier: 3.826A pdb=" N PHE E 388 " --> pdb=" O MET E 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 177 removed outlier: 4.146A pdb=" N ILE F 153 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 154 " --> pdb=" O TRP F 150 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL F 159 " --> pdb=" O SER F 155 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE F 160 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET F 170 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE F 172 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL F 177 " --> pdb=" O VAL F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 221 removed outlier: 3.704A pdb=" N MET F 203 " --> pdb=" O TRP F 199 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU F 205 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE F 210 " --> pdb=" O VAL F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 250 removed outlier: 3.691A pdb=" N THR F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET F 247 " --> pdb=" O ARG F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 281 Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.984A pdb=" N VAL F 303 " --> pdb=" O SER F 299 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU F 305 " --> pdb=" O HIS F 301 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL F 312 " --> pdb=" O LEU F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 341 removed outlier: 3.588A pdb=" N LEU F 339 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 369 removed outlier: 3.725A pdb=" N VAL F 349 " --> pdb=" O TYR F 345 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 355 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 375 removed outlier: 3.707A pdb=" N GLN F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 370 through 375' Processing helix chain 'F' and resid 384 through 389 628 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1830 1.29 - 1.42: 4314 1.42 - 1.56: 7535 1.56 - 1.69: 1 1.69 - 1.83: 174 Bond restraints: 13854 Sorted by residual: bond pdb=" C HIS B 344 " pdb=" O HIS B 344 " ideal model delta sigma weight residual 1.234 1.151 0.083 1.20e-02 6.94e+03 4.75e+01 bond pdb=" C HIS A 344 " pdb=" O HIS A 344 " ideal model delta sigma weight residual 1.234 1.152 0.082 1.20e-02 6.94e+03 4.68e+01 bond pdb=" C19 16C E 500 " pdb=" N2 16C E 500 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C19 16C D 500 " pdb=" N2 16C D 500 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C19 16C A 500 " pdb=" N2 16C A 500 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 ... (remaining 13849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 18389 1.84 - 3.69: 349 3.69 - 5.53: 70 5.53 - 7.38: 10 7.38 - 9.22: 4 Bond angle restraints: 18822 Sorted by residual: angle pdb=" N PRO D 255 " pdb=" CD PRO D 255 " pdb=" CG PRO D 255 " ideal model delta sigma weight residual 103.20 94.63 8.57 1.50e+00 4.44e-01 3.27e+01 angle pdb=" CA PRO D 255 " pdb=" N PRO D 255 " pdb=" CD PRO D 255 " ideal model delta sigma weight residual 112.00 104.14 7.86 1.40e+00 5.10e-01 3.15e+01 angle pdb=" N VAL C 290 " pdb=" CA VAL C 290 " pdb=" C VAL C 290 " ideal model delta sigma weight residual 112.12 107.84 4.28 8.40e-01 1.42e+00 2.59e+01 angle pdb=" N VAL E 290 " pdb=" CA VAL E 290 " pdb=" C VAL E 290 " ideal model delta sigma weight residual 111.62 107.81 3.81 7.90e-01 1.60e+00 2.32e+01 angle pdb=" N GLY F 294 " pdb=" CA GLY F 294 " pdb=" C GLY F 294 " ideal model delta sigma weight residual 112.25 117.13 -4.88 1.34e+00 5.57e-01 1.33e+01 ... (remaining 18817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.41: 7368 24.41 - 48.82: 498 48.82 - 73.23: 51 73.23 - 97.65: 6 97.65 - 122.06: 3 Dihedral angle restraints: 7926 sinusoidal: 3258 harmonic: 4668 Sorted by residual: dihedral pdb=" CB CYS E 261 " pdb=" SG CYS E 261 " pdb=" SG CYS E 293 " pdb=" CB CYS E 293 " ideal model delta sinusoidal sigma weight residual -86.00 -16.39 -69.61 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS C 261 " pdb=" SG CYS C 261 " pdb=" SG CYS C 293 " pdb=" CB CYS C 293 " ideal model delta sinusoidal sigma weight residual 93.00 36.80 56.20 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA CYS F 293 " pdb=" C CYS F 293 " pdb=" N GLY F 294 " pdb=" CA GLY F 294 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 7923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1619 0.046 - 0.092: 357 0.092 - 0.139: 56 0.139 - 0.185: 11 0.185 - 0.231: 9 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C3 16C B 500 " pdb=" C2 16C B 500 " pdb=" C4 16C B 500 " pdb=" O3 16C B 500 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3 16C A 500 " pdb=" C2 16C A 500 " pdb=" C4 16C A 500 " pdb=" O3 16C A 500 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3 16C E 500 " pdb=" C2 16C E 500 " pdb=" C4 16C E 500 " pdb=" O3 16C E 500 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2049 not shown) Planarity restraints: 2262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 343 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C GLU A 343 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU A 343 " 0.020 2.00e-02 2.50e+03 pdb=" N HIS A 344 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 343 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C GLU B 343 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU B 343 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS B 344 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 254 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 255 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 255 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 255 " 0.021 5.00e-02 4.00e+02 ... (remaining 2259 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 626 2.73 - 3.27: 13564 3.27 - 3.82: 20600 3.82 - 4.36: 23678 4.36 - 4.90: 41393 Nonbonded interactions: 99861 Sorted by model distance: nonbonded pdb=" OG SER C 268 " pdb=" OE1 GLU C 271 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASN F 309 " pdb=" OG SER F 327 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR B 372 " pdb=" O VAL B 392 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR F 372 " pdb=" O VAL F 392 " model vdw 2.259 3.040 nonbonded pdb=" OE2 GLU E 148 " pdb=" ND2 ASN E 391 " model vdw 2.270 3.120 ... (remaining 99856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.340 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 13860 Z= 0.215 Angle : 0.624 9.222 18834 Z= 0.338 Chirality : 0.041 0.231 2052 Planarity : 0.004 0.041 2262 Dihedral : 15.195 122.058 4896 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.67 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.21), residues: 1572 helix: -0.04 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.63 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 225 TYR 0.010 0.001 TYR E 213 PHE 0.018 0.001 PHE E 190 TRP 0.008 0.001 TRP A 150 HIS 0.011 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00387 (13854) covalent geometry : angle 0.62399 (18822) SS BOND : bond 0.00477 ( 6) SS BOND : angle 1.11162 ( 12) hydrogen bonds : bond 0.27502 ( 628) hydrogen bonds : angle 6.68362 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.460 Fit side-chains REVERT: A 370 ARG cc_start: 0.7525 (ttm110) cc_final: 0.6899 (ttp80) REVERT: B 296 TYR cc_start: 0.8055 (m-80) cc_final: 0.7799 (m-80) REVERT: C 180 MET cc_start: 0.5433 (tpp) cc_final: 0.4384 (tmm) REVERT: D 224 HIS cc_start: 0.7634 (m-70) cc_final: 0.7143 (m170) REVERT: E 148 GLU cc_start: 0.7445 (mp0) cc_final: 0.7226 (mp0) REVERT: E 183 TYR cc_start: 0.5844 (m-80) cc_final: 0.5632 (m-80) REVERT: E 207 CYS cc_start: 0.8891 (m) cc_final: 0.8484 (m) REVERT: E 224 HIS cc_start: 0.6231 (m170) cc_final: 0.5628 (m170) REVERT: E 350 PHE cc_start: 0.7666 (t80) cc_final: 0.7386 (t80) REVERT: F 151 LYS cc_start: 0.7771 (mttp) cc_final: 0.7298 (mmtp) REVERT: F 180 MET cc_start: 0.4442 (tpt) cc_final: 0.3853 (tmm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.0885 time to fit residues: 35.6835 Evaluate side-chains 234 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS B 344 HIS C 331 ASN E 224 HIS E 301 HIS F 301 HIS F 393 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.198498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134178 restraints weight = 16268.916| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.69 r_work: 0.3370 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13860 Z= 0.150 Angle : 0.595 6.441 18834 Z= 0.320 Chirality : 0.041 0.167 2052 Planarity : 0.004 0.039 2262 Dihedral : 9.362 59.966 1956 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.31 % Favored : 89.57 % Rotamer: Outliers : 1.04 % Allowed : 8.16 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.21), residues: 1572 helix: 1.02 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 225 TYR 0.021 0.001 TYR D 213 PHE 0.025 0.001 PHE E 168 TRP 0.010 0.001 TRP B 150 HIS 0.004 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00327 (13854) covalent geometry : angle 0.59426 (18822) SS BOND : bond 0.00419 ( 6) SS BOND : angle 1.25785 ( 12) hydrogen bonds : bond 0.06983 ( 628) hydrogen bonds : angle 3.66828 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 172 ILE cc_start: 0.8473 (mm) cc_final: 0.8254 (mt) REVERT: A 370 ARG cc_start: 0.7396 (ttm110) cc_final: 0.6813 (ttp80) REVERT: B 213 TYR cc_start: 0.8522 (t80) cc_final: 0.7940 (t80) REVERT: B 314 GLU cc_start: 0.8594 (tp30) cc_final: 0.8193 (tp30) REVERT: C 180 MET cc_start: 0.6024 (tpp) cc_final: 0.4546 (tmm) REVERT: C 241 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8653 (mp) REVERT: D 160 PHE cc_start: 0.6738 (m-80) cc_final: 0.6484 (m-80) REVERT: D 213 TYR cc_start: 0.8962 (t80) cc_final: 0.8749 (t80) REVERT: E 183 TYR cc_start: 0.5923 (m-80) cc_final: 0.5694 (m-80) REVERT: F 180 MET cc_start: 0.5321 (tpt) cc_final: 0.4195 (tmm) REVERT: F 203 MET cc_start: 0.6877 (mmt) cc_final: 0.6660 (mmt) outliers start: 15 outliers final: 14 residues processed: 265 average time/residue: 0.1000 time to fit residues: 39.5692 Evaluate side-chains 251 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 236 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 38 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 134 optimal weight: 0.0020 chunk 18 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN F 393 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.193675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128027 restraints weight = 16512.532| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.63 r_work: 0.3319 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13860 Z= 0.196 Angle : 0.615 6.632 18834 Z= 0.326 Chirality : 0.043 0.168 2052 Planarity : 0.004 0.037 2262 Dihedral : 8.892 59.872 1956 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.50 % Favored : 89.31 % Rotamer: Outliers : 2.21 % Allowed : 11.83 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.21), residues: 1572 helix: 1.17 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.71 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 225 TYR 0.023 0.002 TYR B 296 PHE 0.019 0.002 PHE E 190 TRP 0.010 0.001 TRP B 150 HIS 0.005 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00468 (13854) covalent geometry : angle 0.61451 (18822) SS BOND : bond 0.00474 ( 6) SS BOND : angle 1.30194 ( 12) hydrogen bonds : bond 0.07084 ( 628) hydrogen bonds : angle 3.57437 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.349 Fit side-chains REVERT: A 370 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7051 (ttp80) REVERT: B 213 TYR cc_start: 0.8486 (t80) cc_final: 0.7905 (t80) REVERT: B 314 GLU cc_start: 0.8635 (tp30) cc_final: 0.8424 (tp30) REVERT: C 151 LYS cc_start: 0.8088 (mttp) cc_final: 0.7836 (mttm) REVERT: C 180 MET cc_start: 0.5834 (tpp) cc_final: 0.4444 (tmm) REVERT: C 241 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8644 (mp) REVERT: D 160 PHE cc_start: 0.7003 (m-80) cc_final: 0.6702 (m-80) REVERT: D 203 MET cc_start: 0.7840 (mmt) cc_final: 0.7594 (mpp) REVERT: D 314 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: E 148 GLU cc_start: 0.7998 (mp0) cc_final: 0.7547 (mp0) REVERT: E 180 MET cc_start: 0.7099 (tpp) cc_final: 0.6606 (ttp) REVERT: E 183 TYR cc_start: 0.5891 (m-80) cc_final: 0.5507 (m-80) REVERT: E 314 GLU cc_start: 0.8259 (pp20) cc_final: 0.7905 (pp20) REVERT: E 345 TYR cc_start: 0.8919 (m-80) cc_final: 0.8707 (m-80) REVERT: F 180 MET cc_start: 0.5385 (tpt) cc_final: 0.4260 (tmm) REVERT: F 260 GLN cc_start: 0.7741 (pt0) cc_final: 0.7536 (pm20) outliers start: 32 outliers final: 26 residues processed: 285 average time/residue: 0.0886 time to fit residues: 37.7334 Evaluate side-chains 274 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 117 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 0.0000 chunk 65 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 119 optimal weight: 0.0470 chunk 32 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 0.0570 overall best weight: 0.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.201305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.152899 restraints weight = 16234.260| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.76 r_work: 0.3379 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13860 Z= 0.106 Angle : 0.539 8.099 18834 Z= 0.284 Chirality : 0.039 0.177 2052 Planarity : 0.003 0.033 2262 Dihedral : 8.161 59.816 1956 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.50 % Favored : 89.44 % Rotamer: Outliers : 1.31 % Allowed : 15.42 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1572 helix: 1.56 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.018 0.001 TYR E 266 PHE 0.012 0.001 PHE E 168 TRP 0.009 0.001 TRP B 150 HIS 0.003 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00212 (13854) covalent geometry : angle 0.53814 (18822) SS BOND : bond 0.00379 ( 6) SS BOND : angle 0.97646 ( 12) hydrogen bonds : bond 0.04553 ( 628) hydrogen bonds : angle 3.22763 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.382 Fit side-chains REVERT: A 332 LEU cc_start: 0.8648 (mm) cc_final: 0.8428 (mp) REVERT: A 370 ARG cc_start: 0.7482 (ttm110) cc_final: 0.6790 (ttp80) REVERT: B 213 TYR cc_start: 0.8540 (t80) cc_final: 0.7979 (t80) REVERT: C 151 LYS cc_start: 0.7922 (mttp) cc_final: 0.7697 (mttm) REVERT: D 203 MET cc_start: 0.7936 (mmt) cc_final: 0.7594 (mpp) REVERT: D 212 CYS cc_start: 0.8601 (p) cc_final: 0.8301 (p) REVERT: D 221 LEU cc_start: 0.7792 (mp) cc_final: 0.7468 (tt) REVERT: E 203 MET cc_start: 0.8696 (ppp) cc_final: 0.8478 (tmm) REVERT: E 209 MET cc_start: 0.9484 (mpp) cc_final: 0.9259 (mpp) REVERT: E 212 CYS cc_start: 0.8389 (p) cc_final: 0.8162 (p) REVERT: E 224 HIS cc_start: 0.7922 (m90) cc_final: 0.7645 (m90) REVERT: F 180 MET cc_start: 0.5564 (tpt) cc_final: 0.5146 (tpp) REVERT: F 214 ILE cc_start: 0.8621 (mm) cc_final: 0.8398 (mt) REVERT: F 260 GLN cc_start: 0.7695 (pt0) cc_final: 0.7465 (pm20) outliers start: 19 outliers final: 11 residues processed: 249 average time/residue: 0.0961 time to fit residues: 36.1526 Evaluate side-chains 240 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 319 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 56 optimal weight: 0.0170 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.195396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130009 restraints weight = 16562.038| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.93 r_work: 0.3326 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13860 Z= 0.159 Angle : 0.580 7.960 18834 Z= 0.306 Chirality : 0.041 0.170 2052 Planarity : 0.003 0.036 2262 Dihedral : 8.477 59.933 1956 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.24 % Favored : 89.69 % Rotamer: Outliers : 1.94 % Allowed : 15.77 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.22), residues: 1572 helix: 1.45 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 144 TYR 0.019 0.002 TYR B 296 PHE 0.024 0.001 PHE D 160 TRP 0.009 0.001 TRP A 320 HIS 0.004 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00376 (13854) covalent geometry : angle 0.57946 (18822) SS BOND : bond 0.00457 ( 6) SS BOND : angle 1.10565 ( 12) hydrogen bonds : bond 0.05904 ( 628) hydrogen bonds : angle 3.29964 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7564 (ttm110) cc_final: 0.6839 (ttp80) REVERT: B 213 TYR cc_start: 0.8426 (t80) cc_final: 0.7879 (t80) REVERT: C 151 LYS cc_start: 0.7938 (mttp) cc_final: 0.7647 (mttm) REVERT: C 241 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8621 (mp) REVERT: D 160 PHE cc_start: 0.7194 (m-80) cc_final: 0.6994 (m-80) REVERT: D 203 MET cc_start: 0.7927 (mmt) cc_final: 0.7632 (mpp) REVERT: D 212 CYS cc_start: 0.8633 (p) cc_final: 0.8406 (p) REVERT: E 183 TYR cc_start: 0.6653 (m-80) cc_final: 0.6064 (m-80) REVERT: E 209 MET cc_start: 0.9519 (mpp) cc_final: 0.9271 (mpp) REVERT: E 212 CYS cc_start: 0.8644 (p) cc_final: 0.8395 (p) REVERT: E 213 TYR cc_start: 0.9039 (t80) cc_final: 0.8834 (t80) REVERT: E 314 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8215 (tm-30) REVERT: F 180 MET cc_start: 0.5364 (tpt) cc_final: 0.4187 (tmm) REVERT: F 260 GLN cc_start: 0.7769 (pt0) cc_final: 0.7548 (pm20) outliers start: 28 outliers final: 23 residues processed: 275 average time/residue: 0.0977 time to fit residues: 39.9987 Evaluate side-chains 266 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 143 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.198058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138167 restraints weight = 16343.442| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.81 r_work: 0.3371 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13860 Z= 0.115 Angle : 0.533 7.064 18834 Z= 0.281 Chirality : 0.039 0.169 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.242 59.532 1956 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 1.52 % Allowed : 16.94 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.22), residues: 1572 helix: 1.62 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 379 TYR 0.013 0.001 TYR B 158 PHE 0.017 0.001 PHE E 201 TRP 0.007 0.001 TRP C 270 HIS 0.003 0.001 HIS E 224 Details of bonding type rmsd covalent geometry : bond 0.00253 (13854) covalent geometry : angle 0.53271 (18822) SS BOND : bond 0.00421 ( 6) SS BOND : angle 0.92226 ( 12) hydrogen bonds : bond 0.04865 ( 628) hydrogen bonds : angle 3.16009 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8609 (ttm) cc_final: 0.8387 (mtp) REVERT: A 370 ARG cc_start: 0.7540 (ttm110) cc_final: 0.6838 (ttp80) REVERT: B 213 TYR cc_start: 0.8392 (t80) cc_final: 0.7867 (t80) REVERT: B 314 GLU cc_start: 0.8670 (tp30) cc_final: 0.8460 (tp30) REVERT: B 332 LEU cc_start: 0.8488 (mm) cc_final: 0.8256 (mm) REVERT: C 151 LYS cc_start: 0.7926 (mttp) cc_final: 0.7622 (mttm) REVERT: D 203 MET cc_start: 0.7861 (mmt) cc_final: 0.7554 (mpp) REVERT: D 212 CYS cc_start: 0.8632 (p) cc_final: 0.8411 (p) REVERT: E 168 PHE cc_start: 0.7935 (t80) cc_final: 0.7479 (t80) REVERT: E 183 TYR cc_start: 0.6680 (m-80) cc_final: 0.6121 (m-80) REVERT: E 209 MET cc_start: 0.9459 (mpp) cc_final: 0.9216 (mpp) REVERT: E 212 CYS cc_start: 0.8562 (p) cc_final: 0.8345 (p) REVERT: E 213 TYR cc_start: 0.8947 (t80) cc_final: 0.8678 (t80) REVERT: E 314 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8245 (tm-30) REVERT: F 180 MET cc_start: 0.5327 (tpt) cc_final: 0.4157 (tmm) REVERT: F 314 GLU cc_start: 0.8108 (tp30) cc_final: 0.7860 (tp30) REVERT: F 381 TRP cc_start: 0.8329 (m100) cc_final: 0.8095 (m100) outliers start: 22 outliers final: 16 residues processed: 265 average time/residue: 0.0940 time to fit residues: 37.2097 Evaluate side-chains 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 319 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 153 optimal weight: 0.0000 chunk 146 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS C 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.198002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149310 restraints weight = 16393.155| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 4.20 r_work: 0.3334 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13860 Z= 0.116 Angle : 0.535 6.699 18834 Z= 0.281 Chirality : 0.040 0.177 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.266 59.915 1956 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.07 % Allowed : 16.74 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.22), residues: 1572 helix: 1.65 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.53 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.022 0.001 TYR E 400 PHE 0.020 0.001 PHE E 190 TRP 0.008 0.001 TRP B 270 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00261 (13854) covalent geometry : angle 0.53358 (18822) SS BOND : bond 0.00393 ( 6) SS BOND : angle 1.47554 ( 12) hydrogen bonds : bond 0.04795 ( 628) hydrogen bonds : angle 3.12922 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 TYR cc_start: 0.8445 (t80) cc_final: 0.7915 (t80) REVERT: B 314 GLU cc_start: 0.8708 (tp30) cc_final: 0.8498 (tp30) REVERT: B 332 LEU cc_start: 0.8527 (mm) cc_final: 0.8282 (mm) REVERT: C 151 LYS cc_start: 0.7904 (mttp) cc_final: 0.7617 (mttm) REVERT: C 165 PHE cc_start: 0.8453 (t80) cc_final: 0.7999 (t80) REVERT: C 285 MET cc_start: 0.7494 (mmm) cc_final: 0.7210 (mtp) REVERT: D 203 MET cc_start: 0.7889 (mmt) cc_final: 0.7353 (mpp) REVERT: D 212 CYS cc_start: 0.8727 (p) cc_final: 0.8509 (p) REVERT: E 148 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: E 168 PHE cc_start: 0.7987 (t80) cc_final: 0.7587 (t80) REVERT: E 183 TYR cc_start: 0.6787 (m-80) cc_final: 0.6173 (m-80) REVERT: E 314 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8294 (tm-30) REVERT: E 370 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.6411 (ptt90) REVERT: F 180 MET cc_start: 0.5533 (tpt) cc_final: 0.4284 (tmm) REVERT: F 214 ILE cc_start: 0.8684 (mm) cc_final: 0.8478 (mt) REVERT: F 381 TRP cc_start: 0.8351 (m100) cc_final: 0.8139 (m100) outliers start: 30 outliers final: 22 residues processed: 264 average time/residue: 0.0908 time to fit residues: 35.8052 Evaluate side-chains 259 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 319 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.196164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131521 restraints weight = 16251.834| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.87 r_work: 0.3342 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13860 Z= 0.142 Angle : 0.565 7.637 18834 Z= 0.296 Chirality : 0.041 0.171 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.365 59.677 1956 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 2.35 % Allowed : 16.80 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.22), residues: 1572 helix: 1.54 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.54 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.017 0.001 TYR B 296 PHE 0.018 0.001 PHE E 190 TRP 0.007 0.001 TRP B 270 HIS 0.004 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00333 (13854) covalent geometry : angle 0.56367 (18822) SS BOND : bond 0.00600 ( 6) SS BOND : angle 1.58578 ( 12) hydrogen bonds : bond 0.05336 ( 628) hydrogen bonds : angle 3.22443 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7452 (ttm110) cc_final: 0.6749 (ttp80) REVERT: B 213 TYR cc_start: 0.8404 (t80) cc_final: 0.7892 (t80) REVERT: C 151 LYS cc_start: 0.7851 (mttp) cc_final: 0.7548 (mttm) REVERT: C 165 PHE cc_start: 0.8423 (t80) cc_final: 0.7950 (t80) REVERT: C 241 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8648 (mp) REVERT: D 144 ARG cc_start: 0.4839 (tpt90) cc_final: 0.3375 (mmt180) REVERT: D 203 MET cc_start: 0.7871 (mmt) cc_final: 0.7333 (mpp) REVERT: D 212 CYS cc_start: 0.8746 (p) cc_final: 0.8529 (p) REVERT: E 148 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: E 168 PHE cc_start: 0.7899 (t80) cc_final: 0.7502 (t80) REVERT: E 183 TYR cc_start: 0.6968 (m-80) cc_final: 0.6280 (m-80) REVERT: E 203 MET cc_start: 0.8769 (ppp) cc_final: 0.8460 (tmm) REVERT: E 314 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8226 (tm-30) REVERT: E 370 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.6335 (ptt90) REVERT: F 381 TRP cc_start: 0.8346 (m100) cc_final: 0.8141 (m100) outliers start: 34 outliers final: 28 residues processed: 269 average time/residue: 0.0903 time to fit residues: 35.7963 Evaluate side-chains 269 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.196970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132463 restraints weight = 16370.668| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.89 r_work: 0.3366 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13860 Z= 0.129 Angle : 0.557 9.694 18834 Z= 0.293 Chirality : 0.040 0.190 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.297 59.547 1956 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 2.21 % Allowed : 17.43 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1572 helix: 1.58 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.51 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 225 TYR 0.019 0.001 TYR E 400 PHE 0.017 0.001 PHE E 190 TRP 0.009 0.001 TRP B 270 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00296 (13854) covalent geometry : angle 0.55632 (18822) SS BOND : bond 0.00434 ( 6) SS BOND : angle 1.44265 ( 12) hydrogen bonds : bond 0.05046 ( 628) hydrogen bonds : angle 3.20446 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7483 (ttm110) cc_final: 0.6768 (ttp80) REVERT: B 213 TYR cc_start: 0.8373 (t80) cc_final: 0.7856 (t80) REVERT: B 314 GLU cc_start: 0.8662 (tp30) cc_final: 0.8433 (tp30) REVERT: C 151 LYS cc_start: 0.7890 (mttp) cc_final: 0.7592 (mttp) REVERT: C 165 PHE cc_start: 0.8452 (t80) cc_final: 0.7999 (t80) REVERT: C 241 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8694 (mp) REVERT: D 144 ARG cc_start: 0.4938 (tpt90) cc_final: 0.3437 (mmt180) REVERT: D 203 MET cc_start: 0.7824 (mmt) cc_final: 0.7281 (mpp) REVERT: E 168 PHE cc_start: 0.7940 (t80) cc_final: 0.7598 (t80) REVERT: E 183 TYR cc_start: 0.7185 (m-80) cc_final: 0.6415 (m-80) REVERT: E 203 MET cc_start: 0.8675 (ppp) cc_final: 0.8355 (tmm) REVERT: E 314 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8220 (tm-30) REVERT: E 370 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.6418 (ptt90) REVERT: F 180 MET cc_start: 0.5850 (tpp) cc_final: 0.4636 (tmm) outliers start: 32 outliers final: 27 residues processed: 264 average time/residue: 0.0907 time to fit residues: 35.5261 Evaluate side-chains 262 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.195548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130482 restraints weight = 16193.747| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.62 r_work: 0.3353 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13860 Z= 0.113 Angle : 0.558 9.248 18834 Z= 0.294 Chirality : 0.040 0.182 2052 Planarity : 0.003 0.033 2262 Dihedral : 8.140 59.129 1956 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 1.94 % Allowed : 17.63 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.22), residues: 1572 helix: 1.66 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.46 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 225 TYR 0.018 0.001 TYR E 213 PHE 0.019 0.001 PHE C 248 TRP 0.007 0.001 TRP B 270 HIS 0.003 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00250 (13854) covalent geometry : angle 0.55732 (18822) SS BOND : bond 0.00443 ( 6) SS BOND : angle 1.30123 ( 12) hydrogen bonds : bond 0.04550 ( 628) hydrogen bonds : angle 3.18468 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7367 (ttm110) cc_final: 0.6650 (ttp80) REVERT: B 213 TYR cc_start: 0.8286 (t80) cc_final: 0.7804 (t80) REVERT: B 314 GLU cc_start: 0.8646 (tp30) cc_final: 0.8432 (tp30) REVERT: C 151 LYS cc_start: 0.7739 (mttp) cc_final: 0.7454 (mttp) REVERT: C 165 PHE cc_start: 0.8427 (t80) cc_final: 0.7987 (t80) REVERT: D 144 ARG cc_start: 0.4984 (tpt90) cc_final: 0.3395 (mmt180) REVERT: D 203 MET cc_start: 0.7747 (mmt) cc_final: 0.7191 (mpp) REVERT: E 148 GLU cc_start: 0.7600 (mp0) cc_final: 0.7099 (mp0) REVERT: E 168 PHE cc_start: 0.7889 (t80) cc_final: 0.7563 (t80) REVERT: E 183 TYR cc_start: 0.7004 (m-80) cc_final: 0.6222 (m-80) REVERT: E 203 MET cc_start: 0.8644 (ppp) cc_final: 0.8311 (tmm) REVERT: E 314 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8192 (tm-30) REVERT: E 370 ARG cc_start: 0.7661 (mtm-85) cc_final: 0.6415 (ptt90) outliers start: 28 outliers final: 26 residues processed: 263 average time/residue: 0.1011 time to fit residues: 39.2680 Evaluate side-chains 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 111 optimal weight: 0.0470 chunk 119 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 147 optimal weight: 0.3980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.196738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131834 restraints weight = 16187.082| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.62 r_work: 0.3373 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13860 Z= 0.108 Angle : 0.556 10.203 18834 Z= 0.291 Chirality : 0.039 0.186 2052 Planarity : 0.003 0.033 2262 Dihedral : 7.931 59.390 1956 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 1.73 % Allowed : 17.63 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1572 helix: 1.81 (0.18), residues: 930 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 225 TYR 0.017 0.001 TYR E 400 PHE 0.017 0.001 PHE C 248 TRP 0.007 0.001 TRP A 320 HIS 0.003 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00237 (13854) covalent geometry : angle 0.55538 (18822) SS BOND : bond 0.00426 ( 6) SS BOND : angle 1.26425 ( 12) hydrogen bonds : bond 0.04229 ( 628) hydrogen bonds : angle 3.18093 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2997.97 seconds wall clock time: 52 minutes 4.37 seconds (3124.37 seconds total)