Starting phenix.real_space_refine on Fri May 10 05:00:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/05_2024/8wtz_37847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/05_2024/8wtz_37847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/05_2024/8wtz_37847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/05_2024/8wtz_37847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/05_2024/8wtz_37847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/05_2024/8wtz_37847_updated.pdb" } resolution = 3.1 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= 0.047 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 92 5.16 5 C 9862 2.51 5 N 2433 2.21 5 O 2541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "D GLU 490": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 14930 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3695 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 12, 'TRANS': 434} Chain breaks: 1 Chain: "D" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3650 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3695 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 12, 'TRANS': 434} Chain breaks: 1 Chain: "B" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3654 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 1 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-2': 4, 'PC1:plan-1': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-2': 4, 'PC1:plan-1': 4} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 7.83, per 1000 atoms: 0.52 Number of scatterers: 14930 At special positions: 0 Unit cell: (98.8, 102.96, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 2 15.00 O 2541 8.00 N 2433 7.00 C 9862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 2.6 seconds 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 10 sheets defined 63.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'C' and resid 80 through 106 Proline residue: C 101 - end of helix Processing helix chain 'C' and resid 112 through 134 removed outlier: 4.376A pdb=" N ILE C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU C 117 " --> pdb=" O ASN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.745A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 182 through 207 removed outlier: 4.260A pdb=" N LEU C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARG C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG C 197 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 241 removed outlier: 3.806A pdb=" N LEU C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 removed outlier: 5.028A pdb=" N GLY C 249 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 299 through 328 Processing helix chain 'C' and resid 332 through 348 Processing helix chain 'C' and resid 356 through 378 removed outlier: 3.533A pdb=" N THR C 361 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 362 " --> pdb=" O GLY C 358 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 372 " --> pdb=" O TYR C 368 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 375 " --> pdb=" O SER C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.727A pdb=" N LEU C 395 " --> pdb=" O GLN C 391 " (cutoff:3.500A) Proline residue: C 396 - end of helix removed outlier: 3.701A pdb=" N LYS C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 418 removed outlier: 3.892A pdb=" N ILE C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG C 418 " --> pdb=" O GLN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 499 through 508 Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.553A pdb=" N ARG C 514 " --> pdb=" O PHE C 510 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 106 removed outlier: 3.646A pdb=" N MET D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 91 " --> pdb=" O MET D 87 " (cutoff:3.500A) Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 112 through 134 removed outlier: 4.168A pdb=" N ILE D 116 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.649A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 182 through 207 removed outlier: 3.946A pdb=" N LEU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE D 190 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARG D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG D 197 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 241 removed outlier: 3.718A pdb=" N ALA D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 250 removed outlier: 5.019A pdb=" N GLY D 249 " --> pdb=" O SER D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.604A pdb=" N THR D 276 " --> pdb=" O TRP D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 329 Processing helix chain 'D' and resid 332 through 348 removed outlier: 4.254A pdb=" N ASP D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 343 " --> pdb=" O MET D 340 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D 348 " --> pdb=" O ARG D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 369 removed outlier: 3.543A pdb=" N GLN D 359 " --> pdb=" O ASN D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 380 Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.967A pdb=" N LYS D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) Proline residue: D 396 - end of helix Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 409 through 418 removed outlier: 3.586A pdb=" N ILE D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 478 Processing helix chain 'D' and resid 499 through 508 removed outlier: 3.646A pdb=" N ASN D 504 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 Processing helix chain 'A' and resid 80 through 106 Proline residue: A 101 - end of helix Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.377A pdb=" N ILE A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.745A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 182 through 207 removed outlier: 4.259A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 241 removed outlier: 3.805A pdb=" N LEU A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 5.028A pdb=" N GLY A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 299 through 328 Processing helix chain 'A' and resid 332 through 348 Processing helix chain 'A' and resid 356 through 378 removed outlier: 3.532A pdb=" N THR A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.726A pdb=" N LEU A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) Proline residue: A 396 - end of helix removed outlier: 3.700A pdb=" N LYS A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 418 removed outlier: 3.892A pdb=" N ILE A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG A 418 " --> pdb=" O GLN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 510 through 523 removed outlier: 3.553A pdb=" N ARG A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 106 removed outlier: 3.646A pdb=" N MET B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) Proline residue: B 101 - end of helix Processing helix chain 'B' and resid 112 through 134 removed outlier: 4.168A pdb=" N ILE B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.648A pdb=" N ARG B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 182 through 207 removed outlier: 3.947A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 241 removed outlier: 3.719A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 removed outlier: 5.018A pdb=" N GLY B 249 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.604A pdb=" N THR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 329 Processing helix chain 'B' and resid 332 through 348 removed outlier: 4.254A pdb=" N ASP B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 343 " --> pdb=" O MET B 340 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 348 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 369 removed outlier: 3.543A pdb=" N GLN B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.966A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 409 through 418 removed outlier: 3.586A pdb=" N ILE B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.645A pdb=" N ASN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 Processing sheet with id= A, first strand: chain 'C' and resid 137 through 139 removed outlier: 3.802A pdb=" N TYR C 137 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 146 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 139 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG C 144 " --> pdb=" O ASP C 139 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 420 through 424 removed outlier: 3.555A pdb=" N HIS C 445 " --> pdb=" O ARG C 493 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 495 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL C 443 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C 497 " --> pdb=" O TYR C 441 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TYR C 441 " --> pdb=" O LEU C 497 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 463 through 465 removed outlier: 3.752A pdb=" N ALA C 463 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.564A pdb=" N PHE D 424 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS D 492 " --> pdb=" O PHE D 424 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 463 through 465 removed outlier: 3.732A pdb=" N ALA D 463 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 137 through 139 removed outlier: 3.802A pdb=" N TYR A 137 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 146 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A 139 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A 144 " --> pdb=" O ASP A 139 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 420 through 424 removed outlier: 3.555A pdb=" N HIS A 445 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 495 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL A 443 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 497 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TYR A 441 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 463 through 465 removed outlier: 3.751A pdb=" N ALA A 463 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.563A pdb=" N PHE B 424 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS B 492 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 463 through 465 removed outlier: 3.731A pdb=" N ALA B 463 " --> pdb=" O GLU B 450 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2124 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: 4.30 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2233 1.31 - 1.44: 4380 1.44 - 1.56: 8498 1.56 - 1.69: 8 1.69 - 1.82: 156 Bond restraints: 15275 Sorted by residual: bond pdb=" C TYR B 372 " pdb=" O TYR B 372 " ideal model delta sigma weight residual 1.235 1.412 -0.176 1.26e-02 6.30e+03 1.96e+02 bond pdb=" C TYR D 372 " pdb=" O TYR D 372 " ideal model delta sigma weight residual 1.235 1.411 -0.176 1.26e-02 6.30e+03 1.95e+02 bond pdb=" C VAL B 377 " pdb=" O VAL B 377 " ideal model delta sigma weight residual 1.237 1.337 -0.100 1.14e-02 7.69e+03 7.75e+01 bond pdb=" C VAL D 377 " pdb=" O VAL D 377 " ideal model delta sigma weight residual 1.237 1.336 -0.099 1.14e-02 7.69e+03 7.61e+01 bond pdb=" N ILE B 381 " pdb=" CA ILE B 381 " ideal model delta sigma weight residual 1.461 1.561 -0.100 1.23e-02 6.61e+03 6.61e+01 ... (remaining 15270 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.16: 287 106.16 - 113.17: 7920 113.17 - 120.19: 5854 120.19 - 127.21: 6364 127.21 - 134.23: 150 Bond angle restraints: 20575 Sorted by residual: angle pdb=" N ASP D 380 " pdb=" CA ASP D 380 " pdb=" C ASP D 380 " ideal model delta sigma weight residual 110.06 129.37 -19.31 1.43e+00 4.89e-01 1.82e+02 angle pdb=" O SER D 371 " pdb=" C SER D 371 " pdb=" N TYR D 372 " ideal model delta sigma weight residual 122.59 104.70 17.89 1.33e+00 5.65e-01 1.81e+02 angle pdb=" N ASP B 380 " pdb=" CA ASP B 380 " pdb=" C ASP B 380 " ideal model delta sigma weight residual 110.06 129.27 -19.21 1.43e+00 4.89e-01 1.80e+02 angle pdb=" O SER B 371 " pdb=" C SER B 371 " pdb=" N TYR B 372 " ideal model delta sigma weight residual 122.59 104.85 17.74 1.33e+00 5.65e-01 1.78e+02 angle pdb=" N TYR B 372 " pdb=" CA TYR B 372 " pdb=" C TYR B 372 " ideal model delta sigma weight residual 110.80 129.69 -18.89 2.13e+00 2.20e-01 7.86e+01 ... (remaining 20570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7631 17.98 - 35.97: 1014 35.97 - 53.95: 365 53.95 - 71.94: 55 71.94 - 89.92: 11 Dihedral angle restraints: 9076 sinusoidal: 3822 harmonic: 5254 Sorted by residual: dihedral pdb=" N ASP B 380 " pdb=" C ASP B 380 " pdb=" CA ASP B 380 " pdb=" CB ASP B 380 " ideal model delta harmonic sigma weight residual 122.80 137.50 -14.70 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" N ASP D 380 " pdb=" C ASP D 380 " pdb=" CA ASP D 380 " pdb=" CB ASP D 380 " ideal model delta harmonic sigma weight residual 122.80 137.47 -14.67 0 2.50e+00 1.60e-01 3.44e+01 dihedral pdb=" C ASP B 380 " pdb=" N ASP B 380 " pdb=" CA ASP B 380 " pdb=" CB ASP B 380 " ideal model delta harmonic sigma weight residual -122.60 -136.14 13.54 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 9073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2221 0.145 - 0.290: 33 0.290 - 0.434: 8 0.434 - 0.579: 2 0.579 - 0.724: 2 Chirality restraints: 2266 Sorted by residual: chirality pdb=" CA ASP D 380 " pdb=" N ASP D 380 " pdb=" C ASP D 380 " pdb=" CB ASP D 380 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ASP B 380 " pdb=" N ASP B 380 " pdb=" C ASP B 380 " pdb=" CB ASP B 380 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C2 PC1 C 901 " pdb=" C1 PC1 C 901 " pdb=" C3 PC1 C 901 " pdb=" O21 PC1 C 901 " both_signs ideal model delta sigma weight residual False -2.49 -1.91 -0.58 2.00e-01 2.50e+01 8.35e+00 ... (remaining 2263 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 371 " -0.072 2.00e-02 2.50e+03 1.27e-01 1.60e+02 pdb=" C SER D 371 " 0.219 2.00e-02 2.50e+03 pdb=" O SER D 371 " -0.079 2.00e-02 2.50e+03 pdb=" N TYR D 372 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 371 " 0.072 2.00e-02 2.50e+03 1.26e-01 1.60e+02 pdb=" C SER B 371 " -0.219 2.00e-02 2.50e+03 pdb=" O SER B 371 " 0.079 2.00e-02 2.50e+03 pdb=" N TYR B 372 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 372 " -0.030 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C TYR B 372 " 0.095 2.00e-02 2.50e+03 pdb=" O TYR B 372 " -0.035 2.00e-02 2.50e+03 pdb=" N THR B 373 " -0.030 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 22 2.30 - 2.95: 6616 2.95 - 3.60: 22344 3.60 - 4.25: 35095 4.25 - 4.90: 58164 Nonbonded interactions: 122241 Sorted by model distance: nonbonded pdb=" CE2 TYR C 346 " pdb=" CB ALA B 376 " model vdw 1.650 3.760 nonbonded pdb=" CB ALA D 376 " pdb=" CE2 TYR A 346 " model vdw 1.660 3.760 nonbonded pdb=" CD2 LEU C 364 " pdb=" OD2 ASP B 380 " model vdw 1.830 3.460 nonbonded pdb=" OD2 ASP D 380 " pdb=" CD2 LEU A 364 " model vdw 1.861 3.460 nonbonded pdb=" CD2 TYR C 346 " pdb=" CB ALA B 376 " model vdw 1.980 3.760 ... (remaining 122236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 76 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 524 or (resid 901 and (name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or re \ sid 902 or (resid 903 and (name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38)))) selection = (chain 'B' and (resid 76 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 524 or (resid 901 and (name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or re \ sid 902 or (resid 903 and (name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38)))) selection = (chain 'C' and (resid 76 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 524 or (resid 901 and (name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or re \ sid 902 or (resid 903 and (name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38)))) selection = (chain 'D' and (resid 76 through 524 or (resid 901 and (name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38)) or resid 902 or (resi \ d 903 and (name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.020 Extract box with map and model: 5.410 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.830 Find NCS groups from input model: 0.860 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.006 0.176 15275 Z= 0.376 Angle : 0.849 19.307 20575 Z= 0.523 Chirality : 0.058 0.724 2266 Planarity : 0.006 0.127 2523 Dihedral : 18.201 89.923 5704 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.57 % Allowed : 1.48 % Favored : 97.96 % Rotamer: Outliers : 2.15 % Allowed : 19.99 % Favored : 77.86 % Cbeta Deviations : 0.12 % 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 (0.20), residues: 1762 helix: 0.07 (0.15), residues: 1080 sheet: 0.69 (0.43), residues: 128 loop : 0.34 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 171 HIS 0.009 0.001 HIS A 445 PHE 0.015 0.001 PHE A 115 TYR 0.013 0.001 TYR A 368 ARG 0.006 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 80 ARG cc_start: 0.7162 (ppt170) cc_final: 0.6235 (ptt180) REVERT: C 87 MET cc_start: 0.7855 (mmt) cc_final: 0.7649 (mmt) REVERT: C 183 GLU cc_start: 0.7494 (mp0) cc_final: 0.7054 (pm20) REVERT: C 216 THR cc_start: 0.8431 (t) cc_final: 0.8231 (m) REVERT: C 222 ILE cc_start: 0.8240 (tp) cc_final: 0.7976 (tp) REVERT: C 344 MET cc_start: 0.7239 (mtt) cc_final: 0.6942 (mtt) REVERT: D 87 MET cc_start: 0.8215 (tpp) cc_final: 0.7952 (tpp) REVERT: D 469 HIS cc_start: 0.7636 (m90) cc_final: 0.7374 (m90) REVERT: D 503 MET cc_start: 0.6126 (mpp) cc_final: 0.5891 (mmm) REVERT: A 183 GLU cc_start: 0.7390 (mp0) cc_final: 0.6745 (pm20) REVERT: B 171 TRP cc_start: 0.8330 (m100) cc_final: 0.8068 (m100) REVERT: B 269 ILE cc_start: 0.8419 (mt) cc_final: 0.7796 (mm) REVERT: B 379 GLN cc_start: 0.5072 (OUTLIER) cc_final: 0.4828 (mt0) REVERT: B 422 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6791 (mm-30) REVERT: B 423 PHE cc_start: 0.7019 (m-80) cc_final: 0.6790 (m-80) outliers start: 34 outliers final: 9 residues processed: 240 average time/residue: 0.2722 time to fit residues: 96.1199 Evaluate side-chains 191 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 181 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 379 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15275 Z= 0.216 Angle : 0.589 17.152 20575 Z= 0.297 Chirality : 0.042 0.156 2266 Planarity : 0.005 0.053 2523 Dihedral : 9.600 88.255 2215 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 2.97 % Allowed : 19.35 % Favored : 77.67 % 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: 0.81 (0.20), residues: 1762 helix: 0.77 (0.15), residues: 1086 sheet: -0.03 (0.43), residues: 136 loop : 0.51 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 252 HIS 0.007 0.001 HIS C 445 PHE 0.020 0.001 PHE D 236 TYR 0.014 0.002 TYR D 275 ARG 0.008 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 171 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7573 (mp0) cc_final: 0.7141 (pm20) REVERT: C 222 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7825 (tp) REVERT: C 344 MET cc_start: 0.7640 (mtt) cc_final: 0.7257 (mtt) REVERT: C 370 SER cc_start: 0.5926 (OUTLIER) cc_final: 0.5664 (m) REVERT: D 267 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.6627 (mtm-85) REVERT: D 420 HIS cc_start: 0.6109 (t-170) cc_final: 0.5525 (t-170) REVERT: D 421 GLU cc_start: 0.7585 (pt0) cc_final: 0.7311 (pt0) REVERT: D 469 HIS cc_start: 0.7699 (m90) cc_final: 0.7433 (m90) REVERT: D 480 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6643 (tp) REVERT: A 183 GLU cc_start: 0.7318 (mp0) cc_final: 0.6699 (pm20) REVERT: A 337 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7891 (ttp-170) REVERT: A 370 SER cc_start: 0.6296 (OUTLIER) cc_final: 0.6090 (p) REVERT: A 476 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7294 (mt) REVERT: A 499 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7115 (mmmt) REVERT: B 267 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.6481 (mtm-85) REVERT: B 340 MET cc_start: 0.8391 (mmm) cc_final: 0.8098 (mmt) outliers start: 47 outliers final: 17 residues processed: 208 average time/residue: 0.2771 time to fit residues: 84.7258 Evaluate side-chains 183 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 445 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 485 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 482 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 HIS D 433 GLN D 482 GLN A 445 HIS A 500 GLN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15275 Z= 0.275 Angle : 0.589 18.055 20575 Z= 0.295 Chirality : 0.043 0.150 2266 Planarity : 0.005 0.054 2523 Dihedral : 8.651 84.248 2207 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 3.42 % Allowed : 20.56 % Favored : 76.03 % 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: 1.01 (0.20), residues: 1762 helix: 0.91 (0.15), residues: 1082 sheet: 0.59 (0.45), residues: 116 loop : 0.48 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 272 HIS 0.018 0.001 HIS C 445 PHE 0.021 0.001 PHE B 236 TYR 0.018 0.002 TYR A 275 ARG 0.007 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 169 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7687 (mp0) cc_final: 0.7149 (pm20) REVERT: C 344 MET cc_start: 0.7637 (mtt) cc_final: 0.7248 (mtt) REVERT: C 370 SER cc_start: 0.5853 (OUTLIER) cc_final: 0.5606 (m) REVERT: D 267 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8390 (mtt-85) REVERT: D 347 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8638 (mtm) REVERT: D 469 HIS cc_start: 0.7768 (m90) cc_final: 0.7440 (m90) REVERT: D 480 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6659 (tp) REVERT: A 183 GLU cc_start: 0.7448 (mp0) cc_final: 0.6801 (pm20) REVERT: A 363 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6825 (m-70) REVERT: B 267 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.6696 (mtm-85) REVERT: B 269 ILE cc_start: 0.8528 (mt) cc_final: 0.7873 (mm) REVERT: B 309 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7639 (mm) REVERT: B 323 MET cc_start: 0.8955 (mmt) cc_final: 0.8711 (mmt) outliers start: 54 outliers final: 28 residues processed: 215 average time/residue: 0.3182 time to fit residues: 101.2972 Evaluate side-chains 195 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 30.0000 chunk 152 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 141 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 GLN C 413 ASN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 420 HIS ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15275 Z= 0.157 Angle : 0.524 17.483 20575 Z= 0.258 Chirality : 0.040 0.146 2266 Planarity : 0.004 0.053 2523 Dihedral : 7.952 69.454 2204 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 2.40 % Allowed : 21.19 % Favored : 76.41 % 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: 1.39 (0.20), residues: 1762 helix: 1.25 (0.15), residues: 1080 sheet: 0.59 (0.44), residues: 116 loop : 0.58 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 85 HIS 0.004 0.001 HIS C 230 PHE 0.023 0.001 PHE C 336 TYR 0.010 0.001 TYR C 238 ARG 0.005 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7633 (mp0) cc_final: 0.7125 (pm20) REVERT: C 340 MET cc_start: 0.7401 (ttm) cc_final: 0.6862 (mtt) REVERT: C 344 MET cc_start: 0.7529 (mtt) cc_final: 0.7263 (mtt) REVERT: C 370 SER cc_start: 0.5860 (OUTLIER) cc_final: 0.5622 (m) REVERT: D 267 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.6523 (mtm-85) REVERT: D 309 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7585 (mt) REVERT: D 343 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6804 (mp) REVERT: D 347 MET cc_start: 0.8879 (mtm) cc_final: 0.8657 (mtp) REVERT: D 469 HIS cc_start: 0.7744 (m90) cc_final: 0.7410 (m90) REVERT: D 480 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6750 (tp) REVERT: A 183 GLU cc_start: 0.7377 (mp0) cc_final: 0.6759 (pm20) REVERT: A 499 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7549 (mttt) REVERT: B 267 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.6598 (mtm-85) REVERT: B 269 ILE cc_start: 0.8428 (mt) cc_final: 0.7725 (mm) REVERT: B 309 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7598 (mt) outliers start: 38 outliers final: 14 residues processed: 197 average time/residue: 0.2613 time to fit residues: 77.8192 Evaluate side-chains 179 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 57 optimal weight: 0.0670 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15275 Z= 0.282 Angle : 0.580 17.804 20575 Z= 0.286 Chirality : 0.042 0.149 2266 Planarity : 0.004 0.053 2523 Dihedral : 8.048 59.888 2201 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.38 % Favored : 97.50 % Rotamer: Outliers : 3.10 % Allowed : 21.51 % Favored : 75.40 % 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: 1.19 (0.20), residues: 1762 helix: 1.09 (0.15), residues: 1082 sheet: 0.62 (0.44), residues: 116 loop : 0.50 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 272 HIS 0.021 0.001 HIS A 363 PHE 0.020 0.002 PHE D 236 TYR 0.020 0.002 TYR C 275 ARG 0.007 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 172 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: C 183 GLU cc_start: 0.7646 (mp0) cc_final: 0.7141 (pm20) REVERT: C 340 MET cc_start: 0.7426 (ttm) cc_final: 0.7101 (mtm) REVERT: C 344 MET cc_start: 0.7701 (mtt) cc_final: 0.7415 (mtt) REVERT: D 343 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6985 (mp) REVERT: D 347 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8549 (mtm) REVERT: D 469 HIS cc_start: 0.7713 (m90) cc_final: 0.7262 (m90) REVERT: D 480 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6557 (tp) REVERT: A 183 GLU cc_start: 0.7480 (mp0) cc_final: 0.6826 (pm20) REVERT: A 499 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7663 (mttt) REVERT: B 267 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.6656 (mtm-85) outliers start: 49 outliers final: 29 residues processed: 210 average time/residue: 0.2605 time to fit residues: 81.7165 Evaluate side-chains 197 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 504 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15275 Z= 0.189 Angle : 0.542 17.595 20575 Z= 0.265 Chirality : 0.041 0.146 2266 Planarity : 0.004 0.053 2523 Dihedral : 7.649 59.919 2201 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.16 % Favored : 97.73 % Rotamer: Outliers : 2.78 % Allowed : 21.38 % Favored : 75.84 % 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: 1.40 (0.20), residues: 1762 helix: 1.26 (0.15), residues: 1082 sheet: 0.69 (0.44), residues: 116 loop : 0.56 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 272 HIS 0.014 0.001 HIS A 363 PHE 0.019 0.001 PHE D 236 TYR 0.014 0.001 TYR C 275 ARG 0.006 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 171 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: C 183 GLU cc_start: 0.7586 (mp0) cc_final: 0.6938 (pm20) REVERT: C 344 MET cc_start: 0.7671 (mtt) cc_final: 0.7410 (mtt) REVERT: C 499 LYS cc_start: 0.7860 (mmmm) cc_final: 0.7656 (mmtp) REVERT: D 171 TRP cc_start: 0.8038 (m100) cc_final: 0.7829 (m100) REVERT: D 309 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7629 (mt) REVERT: D 343 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6923 (mp) REVERT: D 349 ARG cc_start: 0.7542 (mtm180) cc_final: 0.7219 (mtm180) REVERT: D 469 HIS cc_start: 0.7713 (m90) cc_final: 0.7227 (m90) REVERT: D 480 ILE cc_start: 0.6835 (OUTLIER) cc_final: 0.6587 (tp) REVERT: A 112 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: A 499 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7728 (mmmm) REVERT: B 139 ASP cc_start: 0.6291 (t70) cc_final: 0.6001 (t70) REVERT: B 309 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7631 (mt) REVERT: B 345 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8109 (mtm-85) outliers start: 44 outliers final: 23 residues processed: 204 average time/residue: 0.2648 time to fit residues: 81.9802 Evaluate side-chains 196 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 104 optimal weight: 0.0970 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN A 413 ASN ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15275 Z= 0.310 Angle : 0.601 17.950 20575 Z= 0.295 Chirality : 0.043 0.147 2266 Planarity : 0.004 0.055 2523 Dihedral : 8.072 59.806 2201 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.05 % Rotamer: Outliers : 3.04 % Allowed : 22.01 % Favored : 74.95 % 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: 1.15 (0.20), residues: 1762 helix: 1.04 (0.15), residues: 1080 sheet: 0.68 (0.44), residues: 116 loop : 0.50 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 272 HIS 0.013 0.001 HIS A 363 PHE 0.026 0.002 PHE C 336 TYR 0.021 0.002 TYR C 275 ARG 0.006 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 176 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: C 183 GLU cc_start: 0.7582 (mp0) cc_final: 0.6962 (pm20) REVERT: C 209 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7447 (mp) REVERT: C 340 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6891 (mmt) REVERT: C 344 MET cc_start: 0.7787 (mtt) cc_final: 0.7550 (mtt) REVERT: D 309 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7616 (mm) REVERT: D 480 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6415 (tp) REVERT: A 112 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: A 145 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.5755 (mmm) REVERT: A 183 GLU cc_start: 0.7516 (mp0) cc_final: 0.6921 (pm20) REVERT: A 209 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 139 ASP cc_start: 0.6058 (t70) cc_final: 0.5772 (t70) REVERT: B 309 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7611 (mm) REVERT: B 503 MET cc_start: 0.6149 (mmm) cc_final: 0.5687 (mpp) outliers start: 48 outliers final: 31 residues processed: 210 average time/residue: 0.2463 time to fit residues: 79.7606 Evaluate side-chains 210 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS C 482 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN A 350 ASN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15275 Z= 0.188 Angle : 0.549 17.756 20575 Z= 0.268 Chirality : 0.041 0.151 2266 Planarity : 0.004 0.055 2523 Dihedral : 7.649 59.960 2201 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 2.72 % Allowed : 22.52 % Favored : 74.76 % 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: 1.42 (0.20), residues: 1762 helix: 1.24 (0.15), residues: 1082 sheet: 0.86 (0.45), residues: 116 loop : 0.60 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 272 HIS 0.012 0.001 HIS A 363 PHE 0.025 0.001 PHE C 336 TYR 0.014 0.001 TYR A 275 ARG 0.009 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 175 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: C 183 GLU cc_start: 0.7515 (mp0) cc_final: 0.6908 (pm20) REVERT: C 209 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7426 (mp) REVERT: C 340 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6959 (mmt) REVERT: C 344 MET cc_start: 0.7750 (mtt) cc_final: 0.7520 (mtt) REVERT: D 309 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7621 (mt) REVERT: D 469 HIS cc_start: 0.7643 (m90) cc_final: 0.7123 (m90) REVERT: D 480 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6647 (tp) REVERT: A 112 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: A 183 GLU cc_start: 0.7440 (mp0) cc_final: 0.6861 (pm20) REVERT: A 209 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 139 ASP cc_start: 0.6127 (t70) cc_final: 0.5858 (t70) REVERT: B 309 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7622 (mt) REVERT: B 421 GLU cc_start: 0.7497 (pt0) cc_final: 0.7270 (pt0) REVERT: B 503 MET cc_start: 0.6185 (mmm) cc_final: 0.5716 (mpp) outliers start: 43 outliers final: 24 residues processed: 207 average time/residue: 0.2423 time to fit residues: 77.0410 Evaluate side-chains 203 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 445 HIS Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 20.0000 chunk 148 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS C 500 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15275 Z= 0.258 Angle : 0.589 17.836 20575 Z= 0.287 Chirality : 0.042 0.151 2266 Planarity : 0.004 0.055 2523 Dihedral : 7.766 59.758 2201 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.38 % Favored : 97.50 % Rotamer: Outliers : 2.34 % Allowed : 22.90 % Favored : 74.76 % 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: 1.31 (0.20), residues: 1762 helix: 1.17 (0.15), residues: 1080 sheet: 0.85 (0.45), residues: 116 loop : 0.54 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 272 HIS 0.013 0.001 HIS A 363 PHE 0.025 0.001 PHE C 336 TYR 0.019 0.002 TYR A 275 ARG 0.010 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 1.581 Fit side-chains revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: C 183 GLU cc_start: 0.7539 (mp0) cc_final: 0.6935 (pm20) REVERT: C 209 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7510 (mp) REVERT: C 340 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6969 (mmt) REVERT: C 344 MET cc_start: 0.7752 (mtt) cc_final: 0.7524 (mtt) REVERT: D 340 MET cc_start: 0.8444 (tpp) cc_final: 0.8231 (mmt) REVERT: D 480 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6860 (tp) REVERT: A 112 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: A 183 GLU cc_start: 0.7469 (mp0) cc_final: 0.6890 (pm20) REVERT: A 209 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7657 (mp) REVERT: B 139 ASP cc_start: 0.6140 (t70) cc_final: 0.5891 (t70) REVERT: B 309 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7622 (mm) REVERT: B 503 MET cc_start: 0.6093 (mmm) cc_final: 0.5629 (mpp) outliers start: 37 outliers final: 24 residues processed: 202 average time/residue: 0.2490 time to fit residues: 76.7992 Evaluate side-chains 204 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 173 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 445 HIS Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 0.0170 chunk 175 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15275 Z= 0.186 Angle : 0.571 17.637 20575 Z= 0.276 Chirality : 0.041 0.145 2266 Planarity : 0.004 0.055 2523 Dihedral : 7.521 59.619 2201 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 2.02 % Allowed : 23.47 % Favored : 74.51 % 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: 1.46 (0.20), residues: 1762 helix: 1.26 (0.15), residues: 1080 sheet: 0.95 (0.45), residues: 116 loop : 0.64 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 272 HIS 0.013 0.001 HIS A 363 PHE 0.024 0.001 PHE C 336 TYR 0.015 0.001 TYR D 372 ARG 0.007 0.000 ARG B 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: C 183 GLU cc_start: 0.7474 (mp0) cc_final: 0.6857 (pm20) REVERT: C 209 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7482 (mp) REVERT: C 269 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8341 (mt) REVERT: C 344 MET cc_start: 0.7717 (mtt) cc_final: 0.7487 (mtt) REVERT: D 469 HIS cc_start: 0.7631 (m90) cc_final: 0.7095 (m90) REVERT: D 480 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6844 (tp) REVERT: D 482 GLN cc_start: 0.6149 (mm110) cc_final: 0.5868 (mm-40) REVERT: A 112 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: A 183 GLU cc_start: 0.7407 (mp0) cc_final: 0.6844 (pm20) REVERT: A 209 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7622 (mp) REVERT: A 334 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6233 (mt-10) REVERT: B 139 ASP cc_start: 0.6152 (t70) cc_final: 0.5906 (t70) REVERT: B 309 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7627 (mt) REVERT: B 345 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.6656 (tmm160) REVERT: B 503 MET cc_start: 0.6085 (mmm) cc_final: 0.5608 (mpp) outliers start: 32 outliers final: 20 residues processed: 200 average time/residue: 0.2615 time to fit residues: 79.2820 Evaluate side-chains 198 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.0980 chunk 42 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.232904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137846 restraints weight = 15110.453| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.18 r_work: 0.3276 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15275 Z= 0.246 Angle : 0.597 17.745 20575 Z= 0.289 Chirality : 0.042 0.160 2266 Planarity : 0.004 0.055 2523 Dihedral : 7.659 59.626 2199 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.21 % Favored : 97.67 % Rotamer: Outliers : 2.02 % Allowed : 23.28 % Favored : 74.70 % 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: 1.33 (0.20), residues: 1762 helix: 1.16 (0.15), residues: 1078 sheet: 0.90 (0.45), residues: 116 loop : 0.58 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 272 HIS 0.013 0.001 HIS A 363 PHE 0.021 0.001 PHE D 236 TYR 0.018 0.002 TYR C 275 ARG 0.007 0.000 ARG B 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.15 seconds wall clock time: 63 minutes 27.57 seconds (3807.57 seconds total)