Starting phenix.real_space_refine on Mon Aug 5 09:45:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9y_37385/08_2024/8w9y_37385.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9y_37385/08_2024/8w9y_37385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9y_37385/08_2024/8w9y_37385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9y_37385/08_2024/8w9y_37385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9y_37385/08_2024/8w9y_37385.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9y_37385/08_2024/8w9y_37385.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.074 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 8790 2.51 5 N 2124 2.21 5 O 2124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 314": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D GLU 314": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 399": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13152 Number of models: 1 Model: "" Number of chains: 6 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} Time building chain proxies: 7.19, per 1000 atoms: 0.55 Number of scatterers: 13152 At special positions: 0 Unit cell: (105.6, 160.6, 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 2124 8.00 N 2124 7.00 C 8790 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.66 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 52 helices and 0 sheets defined 61.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 148 through 175 removed outlier: 3.967A pdb=" N THR A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 221 removed outlier: 4.058A pdb=" N MET A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 250 removed outlier: 3.599A pdb=" N LEU A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 removed outlier: 3.959A pdb=" N LYS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS A 274 " --> pdb=" O TRP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 345 through 370 Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.538A pdb=" N GLN A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 375' Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'B' and resid 150 through 174 removed outlier: 3.696A pdb=" N HIS B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 221 removed outlier: 3.980A pdb=" N MET B 203 " --> pdb=" O TRP B 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 removed outlier: 3.503A pdb=" N LEU B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 Processing helix chain 'B' and resid 299 through 315 removed outlier: 4.076A pdb=" N VAL B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 3.699A pdb=" N LEU B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 370 removed outlier: 3.752A pdb=" N VAL B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'C' and resid 148 through 175 removed outlier: 3.791A pdb=" N THR C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 153 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU C 175 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 221 removed outlier: 4.214A pdb=" N MET C 203 " --> pdb=" O TRP C 199 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 250 removed outlier: 3.925A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.530A pdb=" N HIS C 274 " --> pdb=" O TRP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.744A pdb=" N VAL C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 315 " --> pdb=" O PHE C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 341 removed outlier: 3.506A pdb=" N ILE C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 369 removed outlier: 3.755A pdb=" N VAL C 349 " --> pdb=" O TYR C 345 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 355 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 4.006A pdb=" N SER C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.999A pdb=" N PHE C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 389' Processing helix chain 'D' and resid 150 through 177 removed outlier: 3.945A pdb=" N LEU D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG D 176 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 221 removed outlier: 3.712A pdb=" N MET D 203 " --> pdb=" O TRP D 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 250 removed outlier: 3.622A pdb=" N LEU D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 Processing helix chain 'D' and resid 299 through 315 removed outlier: 3.919A pdb=" N VAL D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 341 removed outlier: 3.566A pdb=" N LEU D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 370 removed outlier: 3.616A pdb=" N ILE D 351 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.753A pdb=" N GLN D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.936A 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 'E' and resid 150 through 175 removed outlier: 3.813A pdb=" N LEU E 154 " --> pdb=" O TRP E 150 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE E 160 " --> pdb=" O CYS E 156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 172 " --> pdb=" O PHE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 221 removed outlier: 3.550A pdb=" N MET E 203 " --> pdb=" O TRP E 199 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 250 removed outlier: 3.578A pdb=" N LEU E 228 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 281 removed outlier: 3.530A pdb=" N HIS E 274 " --> pdb=" O TRP E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.905A pdb=" N VAL E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 341 Processing helix chain 'E' and resid 345 through 370 removed outlier: 3.748A pdb=" N ILE E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 389 removed outlier: 4.101A pdb=" N PHE E 388 " --> pdb=" O MET E 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 175 removed outlier: 3.630A pdb=" N GLU F 175 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 removed outlier: 3.684A pdb=" N SER F 193 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL F 194 " --> pdb=" O PHE F 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 189 through 194' Processing helix chain 'F' and resid 199 through 222 removed outlier: 3.992A pdb=" N MET F 203 " --> pdb=" O TRP F 199 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU F 205 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 250 removed outlier: 3.699A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 281 Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.978A pdb=" N VAL F 303 " --> pdb=" O SER F 299 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL F 312 " --> pdb=" O LEU F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 341 Processing helix chain 'F' and resid 345 through 370 removed outlier: 3.807A pdb=" N VAL F 349 " --> pdb=" O TYR F 345 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 355 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 375 removed outlier: 3.984A pdb=" N SER F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 389 removed outlier: 4.035A pdb=" N PHE F 388 " --> pdb=" O MET F 384 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1977 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: 2.87 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1827 1.32 - 1.44: 4474 1.44 - 1.57: 7150 1.57 - 1.69: 7 1.69 - 1.82: 174 Bond restraints: 13632 Sorted by residual: bond pdb=" CB PRO E 198 " pdb=" CG PRO E 198 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+01 bond pdb=" C PRO C 255 " pdb=" O PRO C 255 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.30e-02 5.92e+03 9.67e+00 bond pdb=" CB PRO C 178 " pdb=" CG PRO C 178 " ideal model delta sigma weight residual 1.492 1.642 -0.150 5.00e-02 4.00e+02 8.98e+00 bond pdb=" CA SER C 253 " pdb=" CB SER C 253 " ideal model delta sigma weight residual 1.532 1.481 0.051 1.74e-02 3.30e+03 8.48e+00 bond pdb=" CB PRO C 185 " pdb=" CG PRO C 185 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.64e+00 ... (remaining 13627 not shown) Histogram of bond angle deviations from ideal: 96.37 - 104.29: 252 104.29 - 112.21: 6735 112.21 - 120.13: 5633 120.13 - 128.05: 5778 128.05 - 135.97: 190 Bond angle restraints: 18588 Sorted by residual: angle pdb=" CA PRO C 185 " pdb=" N PRO C 185 " pdb=" CD PRO C 185 " ideal model delta sigma weight residual 112.00 100.03 11.97 1.40e+00 5.10e-01 7.31e+01 angle pdb=" CA PRO C 178 " pdb=" N PRO C 178 " pdb=" CD PRO C 178 " ideal model delta sigma weight residual 112.00 100.62 11.38 1.40e+00 5.10e-01 6.60e+01 angle pdb=" CA PRO F 403 " pdb=" N PRO F 403 " pdb=" CD PRO F 403 " ideal model delta sigma weight residual 112.00 100.99 11.01 1.40e+00 5.10e-01 6.18e+01 angle pdb=" CA PRO E 198 " pdb=" N PRO E 198 " pdb=" CD PRO E 198 " ideal model delta sigma weight residual 112.00 101.71 10.29 1.40e+00 5.10e-01 5.40e+01 angle pdb=" C PRO C 255 " pdb=" CA PRO C 255 " pdb=" CB PRO C 255 " ideal model delta sigma weight residual 111.56 99.48 12.08 1.65e+00 3.67e-01 5.36e+01 ... (remaining 18583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 6471 16.00 - 32.00: 915 32.00 - 48.01: 271 48.01 - 64.01: 44 64.01 - 80.01: 9 Dihedral angle restraints: 7710 sinusoidal: 3042 harmonic: 4668 Sorted by residual: dihedral pdb=" C PRO C 255 " pdb=" N PRO C 255 " pdb=" CA PRO C 255 " pdb=" CB PRO C 255 " ideal model delta harmonic sigma weight residual -120.70 -104.81 -15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" CA LEU E 186 " pdb=" C LEU E 186 " pdb=" N PRO E 187 " pdb=" CA PRO E 187 " ideal model delta harmonic sigma weight residual -180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA PHE F 388 " pdb=" C PHE F 388 " pdb=" N GLU F 389 " pdb=" CA GLU F 389 " ideal model delta harmonic sigma weight residual -180.00 -162.96 -17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 7707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1808 0.063 - 0.126: 207 0.126 - 0.188: 21 0.188 - 0.251: 2 0.251 - 0.314: 2 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA PRO C 178 " pdb=" N PRO C 178 " pdb=" C PRO C 178 " pdb=" CB PRO C 178 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PRO F 403 " pdb=" N PRO F 403 " pdb=" C PRO F 403 " pdb=" CB PRO F 403 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA PRO C 255 " pdb=" N PRO C 255 " pdb=" C PRO C 255 " pdb=" CB PRO C 255 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2037 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 184 " -0.103 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C 185 " 0.253 5.00e-02 4.00e+02 pdb=" CA PRO C 185 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 185 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 177 " 0.091 5.00e-02 4.00e+02 1.30e-01 2.69e+01 pdb=" N PRO C 178 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 186 " -0.066 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO E 187 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO E 187 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 187 " -0.053 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 144 2.66 - 3.22: 12404 3.22 - 3.78: 19390 3.78 - 4.34: 24764 4.34 - 4.90: 41735 Nonbonded interactions: 98437 Sorted by model distance: nonbonded pdb=" O ILE C 172 " pdb=" NH1 ARG C 176 " model vdw 2.097 3.120 nonbonded pdb=" O PHE E 201 " pdb=" OG1 THR E 204 " model vdw 2.174 3.040 nonbonded pdb=" N GLU D 399 " pdb=" OE1 GLU D 399 " model vdw 2.185 3.120 nonbonded pdb=" OH TYR B 372 " pdb=" O VAL B 392 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 372 " pdb=" O VAL A 392 " model vdw 2.218 3.040 ... (remaining 98432 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: 0.00 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 group one per residue 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: 1.360 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.700 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 0.158 13632 Z= 0.280 Angle : 0.764 15.126 18588 Z= 0.432 Chirality : 0.043 0.314 2040 Planarity : 0.007 0.147 2250 Dihedral : 15.899 80.011 4680 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.48 % Allowed : 21.30 % Favored : 78.22 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1572 helix: 1.33 (0.17), residues: 906 sheet: None (None), residues: 0 loop : -2.76 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 199 HIS 0.004 0.001 HIS E 364 PHE 0.051 0.001 PHE D 277 TYR 0.022 0.001 TYR D 158 ARG 0.002 0.000 ARG C 243 *********************** 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 285 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 278 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 ARG cc_start: 0.8165 (mmp80) cc_final: 0.7963 (mmp80) REVERT: C 393 ASN cc_start: 0.7776 (p0) cc_final: 0.7338 (p0) REVERT: D 151 LYS cc_start: 0.6544 (mttt) cc_final: 0.6214 (mmtt) REVERT: D 402 TRP cc_start: 0.8191 (t-100) cc_final: 0.7735 (t-100) REVERT: E 160 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7043 (t80) REVERT: E 209 MET cc_start: 0.7831 (mmp) cc_final: 0.7345 (mmp) REVERT: E 277 PHE cc_start: 0.6224 (m-80) cc_final: 0.6020 (m-80) REVERT: E 305 LEU cc_start: 0.8700 (mt) cc_final: 0.8475 (mt) REVERT: F 180 MET cc_start: 0.5902 (tmm) cc_final: 0.5627 (tmm) REVERT: F 183 TYR cc_start: 0.5460 (m-80) cc_final: 0.4893 (m-80) REVERT: F 192 ASP cc_start: 0.7151 (m-30) cc_final: 0.6800 (m-30) outliers start: 7 outliers final: 3 residues processed: 281 average time/residue: 0.2164 time to fit residues: 90.9133 Evaluate side-chains 245 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain F residue 165 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS C 291 HIS C 331 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13632 Z= 0.348 Angle : 0.677 10.411 18588 Z= 0.359 Chirality : 0.043 0.185 2040 Planarity : 0.005 0.073 2250 Dihedral : 5.144 50.627 1748 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 4.36 % Allowed : 19.23 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1572 helix: 1.44 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.77 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 402 HIS 0.005 0.001 HIS E 342 PHE 0.029 0.002 PHE B 298 TYR 0.018 0.002 TYR F 149 ARG 0.004 0.000 ARG F 275 *********************** 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 317 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 254 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 172 ILE cc_start: 0.8858 (mm) cc_final: 0.8426 (mt) REVERT: C 393 ASN cc_start: 0.7392 (p0) cc_final: 0.7178 (p0) REVERT: D 160 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: D 402 TRP cc_start: 0.8196 (t-100) cc_final: 0.7698 (t-100) REVERT: E 160 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.7243 (t80) REVERT: E 209 MET cc_start: 0.7876 (mmp) cc_final: 0.7439 (mmp) REVERT: E 248 PHE cc_start: 0.8547 (t80) cc_final: 0.8344 (t80) REVERT: E 336 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7742 (t80) REVERT: F 315 TYR cc_start: 0.7069 (m-80) cc_final: 0.6580 (m-80) REVERT: F 398 ASN cc_start: 0.4372 (p0) cc_final: 0.3673 (p0) outliers start: 63 outliers final: 36 residues processed: 294 average time/residue: 0.2112 time to fit residues: 93.7831 Evaluate side-chains 269 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 PHE Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 400 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN C 222 HIS C 331 ASN C 398 ASN ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13632 Z= 0.282 Angle : 0.620 12.799 18588 Z= 0.326 Chirality : 0.041 0.197 2040 Planarity : 0.005 0.064 2250 Dihedral : 4.936 51.163 1744 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 4.50 % Allowed : 21.23 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1572 helix: 1.68 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.72 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 402 HIS 0.005 0.001 HIS E 342 PHE 0.037 0.002 PHE E 277 TYR 0.019 0.002 TYR E 158 ARG 0.003 0.000 ARG E 379 *********************** 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 324 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 259 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7477 (mm-30) REVERT: B 271 GLU cc_start: 0.7847 (tp30) cc_final: 0.7611 (tp30) REVERT: B 343 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7768 (mm-30) REVERT: C 172 ILE cc_start: 0.8794 (mm) cc_final: 0.8433 (mt) REVERT: C 176 ARG cc_start: 0.8477 (mmp80) cc_final: 0.7904 (mmp80) REVERT: C 370 ARG cc_start: 0.6498 (ptt-90) cc_final: 0.6082 (ptt90) REVERT: D 209 MET cc_start: 0.8125 (mmm) cc_final: 0.7631 (mmm) REVERT: D 215 TRP cc_start: 0.8568 (t-100) cc_final: 0.7972 (t-100) REVERT: D 402 TRP cc_start: 0.8233 (t-100) cc_final: 0.7626 (t-100) REVERT: E 160 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7379 (t80) REVERT: E 209 MET cc_start: 0.8157 (mmp) cc_final: 0.7759 (mmp) REVERT: E 336 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7832 (t80) REVERT: F 151 LYS cc_start: 0.6154 (mtpt) cc_final: 0.5456 (ptmt) REVERT: F 183 TYR cc_start: 0.5930 (OUTLIER) cc_final: 0.4800 (m-80) REVERT: F 398 ASN cc_start: 0.4972 (p0) cc_final: 0.4485 (p0) outliers start: 65 outliers final: 40 residues processed: 300 average time/residue: 0.2149 time to fit residues: 96.2607 Evaluate side-chains 277 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 234 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 0.0770 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13632 Z= 0.183 Angle : 0.573 12.305 18588 Z= 0.300 Chirality : 0.039 0.181 2040 Planarity : 0.004 0.055 2250 Dihedral : 4.525 51.025 1742 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 3.80 % Allowed : 22.54 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1572 helix: 2.02 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.62 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 402 HIS 0.009 0.001 HIS A 174 PHE 0.025 0.001 PHE D 201 TYR 0.017 0.001 TYR E 158 ARG 0.003 0.000 ARG E 379 *********************** 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 321 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 266 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7604 (mm-30) REVERT: A 297 MET cc_start: 0.8322 (tpt) cc_final: 0.7951 (mmm) REVERT: B 181 GLN cc_start: 0.8133 (pp30) cc_final: 0.7544 (mm-40) REVERT: B 271 GLU cc_start: 0.7900 (tp30) cc_final: 0.7608 (tp30) REVERT: B 343 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7675 (mm-30) REVERT: C 172 ILE cc_start: 0.8766 (mm) cc_final: 0.8481 (mt) REVERT: C 176 ARG cc_start: 0.8308 (mmp80) cc_final: 0.7841 (mmp80) REVERT: C 370 ARG cc_start: 0.6331 (ptt-90) cc_final: 0.5679 (ptt90) REVERT: C 384 MET cc_start: 0.6436 (mmm) cc_final: 0.6218 (tpp) REVERT: C 393 ASN cc_start: 0.7609 (p0) cc_final: 0.7392 (p0) REVERT: D 209 MET cc_start: 0.8344 (mmm) cc_final: 0.7888 (mmm) REVERT: D 215 TRP cc_start: 0.8527 (t-100) cc_final: 0.7965 (t-100) REVERT: D 402 TRP cc_start: 0.8130 (t-100) cc_final: 0.7610 (t-100) REVERT: E 160 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: E 209 MET cc_start: 0.8152 (mmp) cc_final: 0.7773 (mmp) REVERT: E 247 MET cc_start: 0.7544 (mmt) cc_final: 0.7338 (mmp) REVERT: E 336 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7792 (t80) REVERT: E 370 ARG cc_start: 0.7721 (tmt-80) cc_final: 0.7422 (tmt-80) REVERT: F 151 LYS cc_start: 0.6251 (mtpt) cc_final: 0.5536 (ptmt) REVERT: F 183 TYR cc_start: 0.5808 (OUTLIER) cc_final: 0.4651 (m-80) REVERT: F 275 ARG cc_start: 0.5675 (tpt170) cc_final: 0.5409 (tpt170) outliers start: 55 outliers final: 40 residues processed: 305 average time/residue: 0.2155 time to fit residues: 98.3374 Evaluate side-chains 284 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 241 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 128 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 0.0070 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 398 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13632 Z= 0.226 Angle : 0.598 14.569 18588 Z= 0.311 Chirality : 0.040 0.197 2040 Planarity : 0.004 0.048 2250 Dihedral : 4.497 50.696 1742 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 4.84 % Allowed : 22.20 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1572 helix: 1.97 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 402 HIS 0.006 0.001 HIS A 174 PHE 0.027 0.001 PHE D 201 TYR 0.018 0.001 TYR E 158 ARG 0.003 0.000 ARG E 379 *********************** 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 325 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 255 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 264 LYS cc_start: 0.7858 (mppt) cc_final: 0.7307 (tttp) REVERT: B 271 GLU cc_start: 0.7916 (tp30) cc_final: 0.7614 (tp30) REVERT: B 343 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7744 (mm-30) REVERT: C 172 ILE cc_start: 0.8799 (mm) cc_final: 0.8491 (mt) REVERT: C 384 MET cc_start: 0.6530 (mmm) cc_final: 0.6149 (mtt) REVERT: C 393 ASN cc_start: 0.7786 (p0) cc_final: 0.7472 (p0) REVERT: D 160 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: D 209 MET cc_start: 0.8340 (mmm) cc_final: 0.7852 (mmm) REVERT: D 215 TRP cc_start: 0.8534 (t-100) cc_final: 0.7864 (t-100) REVERT: D 402 TRP cc_start: 0.8134 (t-100) cc_final: 0.7594 (t-100) REVERT: E 160 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7029 (m-80) REVERT: E 209 MET cc_start: 0.8114 (mmp) cc_final: 0.7773 (mmp) REVERT: E 336 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7822 (t80) REVERT: F 151 LYS cc_start: 0.6311 (mtpt) cc_final: 0.5595 (ptmt) REVERT: F 183 TYR cc_start: 0.5901 (OUTLIER) cc_final: 0.4645 (m-80) outliers start: 70 outliers final: 55 residues processed: 306 average time/residue: 0.2074 time to fit residues: 96.6137 Evaluate side-chains 300 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 241 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.0060 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13632 Z= 0.187 Angle : 0.577 14.105 18588 Z= 0.302 Chirality : 0.039 0.181 2040 Planarity : 0.004 0.044 2250 Dihedral : 4.405 50.343 1742 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 4.56 % Allowed : 23.03 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1572 helix: 2.10 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 402 HIS 0.005 0.001 HIS A 174 PHE 0.013 0.001 PHE E 190 TYR 0.012 0.001 TYR A 158 ARG 0.002 0.000 ARG F 243 *********************** 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 315 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 249 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 264 LYS cc_start: 0.7808 (mppt) cc_final: 0.7369 (tttp) REVERT: B 271 GLU cc_start: 0.7896 (tp30) cc_final: 0.7575 (tp30) REVERT: C 172 ILE cc_start: 0.8757 (mm) cc_final: 0.8552 (mt) REVERT: C 384 MET cc_start: 0.6624 (mmm) cc_final: 0.6300 (mtt) REVERT: C 393 ASN cc_start: 0.7706 (p0) cc_final: 0.7384 (p0) REVERT: D 160 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: D 209 MET cc_start: 0.8307 (mmm) cc_final: 0.7915 (mmm) REVERT: D 215 TRP cc_start: 0.8482 (t-100) cc_final: 0.8011 (t-100) REVERT: D 402 TRP cc_start: 0.8053 (t-100) cc_final: 0.7545 (t-100) REVERT: E 209 MET cc_start: 0.8135 (mmp) cc_final: 0.7877 (mmm) REVERT: E 272 LYS cc_start: 0.7782 (mtpp) cc_final: 0.7554 (mtmm) REVERT: E 336 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7753 (t80) REVERT: F 151 LYS cc_start: 0.6399 (mtpt) cc_final: 0.5623 (ptmt) REVERT: F 183 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.4552 (m-80) REVERT: F 248 PHE cc_start: 0.8386 (t80) cc_final: 0.8143 (t80) outliers start: 66 outliers final: 51 residues processed: 298 average time/residue: 0.2070 time to fit residues: 94.9321 Evaluate side-chains 290 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.0070 chunk 93 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN C 398 ASN F 174 HIS ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13632 Z= 0.179 Angle : 0.571 14.624 18588 Z= 0.299 Chirality : 0.039 0.178 2040 Planarity : 0.004 0.042 2250 Dihedral : 4.149 19.199 1740 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.50 % Allowed : 23.58 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1572 helix: 2.14 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 402 HIS 0.006 0.001 HIS A 174 PHE 0.012 0.001 PHE E 190 TYR 0.019 0.001 TYR E 315 ARG 0.004 0.000 ARG F 243 *********************** 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 317 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 252 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 347 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7083 (pt) REVERT: B 264 LYS cc_start: 0.7715 (mppt) cc_final: 0.7360 (tttp) REVERT: B 271 GLU cc_start: 0.7830 (tp30) cc_final: 0.7511 (tp30) REVERT: C 172 ILE cc_start: 0.8826 (mm) cc_final: 0.8615 (mt) REVERT: C 384 MET cc_start: 0.6572 (mmm) cc_final: 0.6260 (mtt) REVERT: C 393 ASN cc_start: 0.7676 (p0) cc_final: 0.7315 (p0) REVERT: D 160 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: D 209 MET cc_start: 0.8368 (mmm) cc_final: 0.7948 (mmm) REVERT: D 215 TRP cc_start: 0.8505 (t-100) cc_final: 0.8082 (t-100) REVERT: D 402 TRP cc_start: 0.8058 (t-100) cc_final: 0.7553 (t-100) REVERT: E 160 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: E 205 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7271 (mm-30) REVERT: E 209 MET cc_start: 0.8143 (mmp) cc_final: 0.7882 (mmm) REVERT: E 247 MET cc_start: 0.7416 (mmt) cc_final: 0.7164 (mmp) REVERT: E 272 LYS cc_start: 0.7725 (mtpp) cc_final: 0.7501 (mtmm) REVERT: E 336 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7822 (t80) REVERT: F 151 LYS cc_start: 0.6470 (mtpt) cc_final: 0.5622 (ptmt) REVERT: F 183 TYR cc_start: 0.5838 (OUTLIER) cc_final: 0.4467 (m-80) outliers start: 65 outliers final: 51 residues processed: 300 average time/residue: 0.2013 time to fit residues: 91.8370 Evaluate side-chains 294 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 238 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 199 TRP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 118 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13632 Z= 0.179 Angle : 0.568 15.179 18588 Z= 0.299 Chirality : 0.039 0.177 2040 Planarity : 0.004 0.040 2250 Dihedral : 4.091 19.341 1740 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 4.22 % Allowed : 24.00 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1572 helix: 2.18 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.48 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 402 HIS 0.006 0.001 HIS A 174 PHE 0.015 0.001 PHE F 160 TYR 0.019 0.001 TYR D 158 ARG 0.002 0.000 ARG D 370 *********************** 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 309 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 248 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 264 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.6080 (mptt) REVERT: A 347 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7229 (pt) REVERT: B 264 LYS cc_start: 0.7674 (mppt) cc_final: 0.7329 (tttp) REVERT: B 343 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7547 (mm-30) REVERT: C 172 ILE cc_start: 0.8835 (mm) cc_final: 0.8625 (mt) REVERT: C 192 ASP cc_start: 0.7387 (m-30) cc_final: 0.7182 (m-30) REVERT: C 384 MET cc_start: 0.6650 (mmm) cc_final: 0.6290 (mtt) REVERT: C 393 ASN cc_start: 0.7691 (p0) cc_final: 0.7308 (p0) REVERT: D 209 MET cc_start: 0.8387 (mmm) cc_final: 0.8008 (mmm) REVERT: D 215 TRP cc_start: 0.8498 (t-100) cc_final: 0.8100 (t-100) REVERT: D 399 GLU cc_start: 0.5408 (pm20) cc_final: 0.5147 (pm20) REVERT: D 402 TRP cc_start: 0.7998 (t-100) cc_final: 0.7525 (t-100) REVERT: E 160 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: E 205 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7199 (mm-30) REVERT: E 209 MET cc_start: 0.8171 (mmp) cc_final: 0.7913 (mmm) REVERT: E 336 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7822 (t80) REVERT: F 151 LYS cc_start: 0.6468 (mtpt) cc_final: 0.5608 (ptmt) REVERT: F 183 TYR cc_start: 0.5838 (OUTLIER) cc_final: 0.4639 (m-80) REVERT: F 364 HIS cc_start: 0.6091 (OUTLIER) cc_final: 0.5523 (t70) REVERT: F 398 ASN cc_start: 0.5908 (p0) cc_final: 0.5414 (t0) outliers start: 61 outliers final: 49 residues processed: 292 average time/residue: 0.2066 time to fit residues: 91.8725 Evaluate side-chains 292 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13632 Z= 0.203 Angle : 0.586 15.488 18588 Z= 0.307 Chirality : 0.039 0.176 2040 Planarity : 0.004 0.040 2250 Dihedral : 4.125 19.675 1740 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 4.29 % Allowed : 24.90 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1572 helix: 2.14 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 402 HIS 0.006 0.001 HIS A 174 PHE 0.022 0.001 PHE B 387 TYR 0.019 0.001 TYR D 158 ARG 0.006 0.000 ARG F 176 *********************** 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 309 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 247 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 181 GLN cc_start: 0.8090 (pp30) cc_final: 0.7772 (pp30) REVERT: A 264 LYS cc_start: 0.6329 (OUTLIER) cc_final: 0.6067 (mptt) REVERT: A 347 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7153 (pt) REVERT: B 264 LYS cc_start: 0.7693 (mppt) cc_final: 0.7344 (tttp) REVERT: B 271 GLU cc_start: 0.7639 (tp30) cc_final: 0.7439 (tp30) REVERT: C 172 ILE cc_start: 0.8805 (mm) cc_final: 0.8590 (mt) REVERT: C 192 ASP cc_start: 0.7396 (m-30) cc_final: 0.7192 (m-30) REVERT: C 393 ASN cc_start: 0.7427 (p0) cc_final: 0.7099 (p0) REVERT: D 209 MET cc_start: 0.8410 (mmm) cc_final: 0.8051 (mmm) REVERT: D 215 TRP cc_start: 0.8494 (t-100) cc_final: 0.8116 (t-100) REVERT: D 399 GLU cc_start: 0.5386 (pm20) cc_final: 0.5093 (pm20) REVERT: D 402 TRP cc_start: 0.7977 (t-100) cc_final: 0.7478 (t-100) REVERT: E 160 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7222 (m-80) REVERT: E 205 GLU cc_start: 0.7666 (mm-30) cc_final: 0.6845 (mm-30) REVERT: E 209 MET cc_start: 0.8183 (mmp) cc_final: 0.7911 (mmm) REVERT: E 285 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5861 (mpp) REVERT: E 336 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7847 (t80) REVERT: F 151 LYS cc_start: 0.6756 (mtpt) cc_final: 0.5858 (ptmt) REVERT: F 183 TYR cc_start: 0.5798 (OUTLIER) cc_final: 0.4681 (m-80) REVERT: F 248 PHE cc_start: 0.8417 (t80) cc_final: 0.8158 (t80) REVERT: F 364 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5548 (t70) REVERT: F 398 ASN cc_start: 0.5981 (p0) cc_final: 0.5614 (t0) outliers start: 62 outliers final: 52 residues processed: 295 average time/residue: 0.2148 time to fit residues: 96.3745 Evaluate side-chains 297 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 238 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 199 TRP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 155 optimal weight: 0.0370 chunk 143 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN C 364 HIS ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13632 Z= 0.188 Angle : 0.595 15.961 18588 Z= 0.309 Chirality : 0.039 0.179 2040 Planarity : 0.004 0.039 2250 Dihedral : 4.123 19.566 1740 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 4.22 % Allowed : 25.24 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1572 helix: 2.16 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.48 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 402 HIS 0.006 0.001 HIS C 291 PHE 0.020 0.001 PHE B 387 TYR 0.019 0.001 TYR D 158 ARG 0.003 0.000 ARG F 243 ********************** 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 310 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 249 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 181 GLN cc_start: 0.8108 (pp30) cc_final: 0.7787 (pp30) REVERT: A 264 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.6058 (mptt) REVERT: A 347 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7150 (pt) REVERT: B 260 GLN cc_start: 0.7945 (tt0) cc_final: 0.7693 (tm-30) REVERT: B 264 LYS cc_start: 0.7644 (mppt) cc_final: 0.7320 (tttp) REVERT: C 172 ILE cc_start: 0.8761 (mm) cc_final: 0.8553 (mt) REVERT: C 192 ASP cc_start: 0.7385 (m-30) cc_final: 0.7183 (m-30) REVERT: C 199 TRP cc_start: 0.7390 (p-90) cc_final: 0.7189 (p-90) REVERT: C 393 ASN cc_start: 0.7421 (p0) cc_final: 0.7114 (p0) REVERT: D 209 MET cc_start: 0.8397 (mmm) cc_final: 0.8029 (mmm) REVERT: D 215 TRP cc_start: 0.8490 (t-100) cc_final: 0.8117 (t-100) REVERT: D 399 GLU cc_start: 0.5241 (pm20) cc_final: 0.4948 (pm20) REVERT: D 402 TRP cc_start: 0.7936 (t-100) cc_final: 0.7469 (t-100) REVERT: E 160 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: E 205 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6538 (mm-30) REVERT: E 209 MET cc_start: 0.8202 (mmp) cc_final: 0.7888 (mmm) REVERT: E 285 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5863 (mpp) REVERT: E 336 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7852 (t80) REVERT: F 151 LYS cc_start: 0.6723 (mtpt) cc_final: 0.5798 (ptmt) REVERT: F 183 TYR cc_start: 0.5652 (OUTLIER) cc_final: 0.4494 (m-80) REVERT: F 248 PHE cc_start: 0.8432 (t80) cc_final: 0.8179 (t80) REVERT: F 364 HIS cc_start: 0.6046 (OUTLIER) cc_final: 0.5525 (t70) REVERT: F 398 ASN cc_start: 0.5851 (p0) cc_final: 0.5553 (t0) outliers start: 61 outliers final: 51 residues processed: 292 average time/residue: 0.2007 time to fit residues: 89.5646 Evaluate side-chains 298 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 240 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 199 TRP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN D 364 HIS ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.211396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143622 restraints weight = 16766.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143462 restraints weight = 9852.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142671 restraints weight = 8249.070| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13632 Z= 0.202 Angle : 0.602 15.920 18588 Z= 0.315 Chirality : 0.040 0.197 2040 Planarity : 0.004 0.039 2250 Dihedral : 4.124 19.702 1740 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 4.01 % Allowed : 25.59 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1572 helix: 2.09 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.48 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 402 HIS 0.006 0.001 HIS C 291 PHE 0.020 0.001 PHE B 387 TYR 0.018 0.001 TYR D 158 ARG 0.002 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.80 seconds wall clock time: 48 minutes 23.83 seconds (2903.83 seconds total)