Starting phenix.real_space_refine on Fri Mar 15 21:43:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/03_2024/3jae_6345.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/03_2024/3jae_6345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/03_2024/3jae_6345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/03_2024/3jae_6345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/03_2024/3jae_6345.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/03_2024/3jae_6345.pdb" } resolution = 3.9 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8360 2.51 5 N 2130 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 343": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 343": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12825 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2537 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2537 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2537 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2537 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "E" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2537 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.64, per 1000 atoms: 0.60 Number of scatterers: 12825 At special positions: 0 Unit cell: (96.0324, 98.4636, 127.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2270 8.00 N 2130 7.00 C 8360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 2.3 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 39.7% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.132A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 235 through 243 removed outlier: 4.666A pdb=" N TYR A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.906A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 288 removed outlier: 4.411A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 363 removed outlier: 3.751A pdb=" N THR A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.897A pdb=" N ILE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.132A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 235 through 243 removed outlier: 4.665A pdb=" N TYR B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 260 removed outlier: 3.907A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 288 removed outlier: 4.411A pdb=" N ARG B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 363 removed outlier: 3.751A pdb=" N THR B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Proline residue: B 347 - end of helix removed outlier: 3.897A pdb=" N ILE B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.133A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 235 through 243 removed outlier: 4.666A pdb=" N TYR C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 260 removed outlier: 3.906A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 288 removed outlier: 4.410A pdb=" N ARG C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 363 removed outlier: 3.752A pdb=" N THR C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Proline residue: C 347 - end of helix removed outlier: 3.897A pdb=" N ILE C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR C 360 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 361 " --> pdb=" O TYR C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.132A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 235 through 243 removed outlier: 4.665A pdb=" N TYR D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 260 removed outlier: 3.906A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 288 removed outlier: 4.410A pdb=" N ARG D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 288 " --> pdb=" O SER D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 363 removed outlier: 3.752A pdb=" N THR D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Proline residue: D 347 - end of helix removed outlier: 3.897A pdb=" N ILE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR D 360 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR D 361 " --> pdb=" O TYR D 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.132A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 235 through 243 removed outlier: 4.665A pdb=" N TYR E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 260 removed outlier: 3.907A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL E 256 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 288 removed outlier: 4.411A pdb=" N ARG E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER E 286 " --> pdb=" O GLN E 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 288 " --> pdb=" O SER E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 363 removed outlier: 3.751A pdb=" N THR E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Proline residue: E 347 - end of helix removed outlier: 3.897A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR E 360 " --> pdb=" O PHE E 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR E 361 " --> pdb=" O TYR E 357 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.931A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.932A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.932A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.932A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.931A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2373 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: 4.21 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3892 1.34 - 1.46: 2535 1.46 - 1.58: 6613 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 13145 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 13140 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.24: 492 107.24 - 113.92: 7191 113.92 - 120.60: 5052 120.60 - 127.28: 5105 127.28 - 133.96: 135 Bond angle restraints: 17975 Sorted by residual: angle pdb=" C THR D 128 " pdb=" CA THR D 128 " pdb=" CB THR D 128 " ideal model delta sigma weight residual 116.63 109.43 7.20 1.16e+00 7.43e-01 3.85e+01 angle pdb=" C THR B 128 " pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 116.63 109.43 7.20 1.16e+00 7.43e-01 3.85e+01 angle pdb=" C THR E 128 " pdb=" CA THR E 128 " pdb=" CB THR E 128 " ideal model delta sigma weight residual 116.63 109.45 7.18 1.16e+00 7.43e-01 3.83e+01 angle pdb=" C THR A 128 " pdb=" CA THR A 128 " pdb=" CB THR A 128 " ideal model delta sigma weight residual 116.63 109.47 7.16 1.16e+00 7.43e-01 3.81e+01 angle pdb=" N GLU E 119 " pdb=" CA GLU E 119 " pdb=" C GLU E 119 " ideal model delta sigma weight residual 111.33 118.79 -7.46 1.21e+00 6.83e-01 3.80e+01 ... (remaining 17970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 7540 16.88 - 33.76: 250 33.76 - 50.63: 20 50.63 - 67.51: 15 67.51 - 84.39: 5 Dihedral angle restraints: 7830 sinusoidal: 2840 harmonic: 4990 Sorted by residual: dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -149.65 63.65 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " pdb=" CB CYS D 225 " ideal model delta sinusoidal sigma weight residual -86.00 -149.64 63.64 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS E 214 " pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " pdb=" CB CYS E 225 " ideal model delta sinusoidal sigma weight residual -86.00 -149.62 63.62 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 7827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1317 0.037 - 0.074: 602 0.074 - 0.112: 157 0.112 - 0.149: 49 0.149 - 0.186: 5 Chirality restraints: 2130 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.18e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.60e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.45e+00 ... (remaining 2127 not shown) Planarity restraints: 2245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 115 " -0.020 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE C 115 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE C 115 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE C 115 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 115 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 115 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE C 115 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 115 " 0.020 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE E 115 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE E 115 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE E 115 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 115 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 115 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE E 115 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 115 " 0.020 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE A 115 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 115 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 115 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 115 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 115 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 115 " -0.003 2.00e-02 2.50e+03 ... (remaining 2242 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1005 2.74 - 3.28: 13587 3.28 - 3.82: 20380 3.82 - 4.36: 23800 4.36 - 4.90: 40392 Nonbonded interactions: 99164 Sorted by model distance: nonbonded pdb=" OG1 THR A 128 " pdb=" O LEU E 114 " model vdw 2.202 2.440 nonbonded pdb=" O VAL B 251 " pdb=" OG SER B 254 " model vdw 2.228 2.440 nonbonded pdb=" O VAL D 251 " pdb=" OG SER D 254 " model vdw 2.229 2.440 nonbonded pdb=" O VAL E 251 " pdb=" OG SER E 254 " model vdw 2.229 2.440 nonbonded pdb=" O VAL A 251 " pdb=" OG SER A 254 " model vdw 2.229 2.440 ... (remaining 99159 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.010 Extract box with map and model: 3.750 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 36.950 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 0.049 13145 Z= 0.417 Angle : 1.255 7.985 17975 Z= 0.839 Chirality : 0.046 0.186 2130 Planarity : 0.006 0.059 2245 Dihedral : 9.721 84.390 4575 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 1670 helix: -1.72 (0.19), residues: 510 sheet: 0.50 (0.26), residues: 375 loop : -1.46 (0.17), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP A 255 HIS 0.004 0.002 HIS B 125 PHE 0.054 0.004 PHE E 115 TYR 0.047 0.003 TYR B 74 ARG 0.015 0.002 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LYS cc_start: 0.8107 (mttm) cc_final: 0.7869 (mtmt) REVERT: A 204 ILE cc_start: 0.8672 (pt) cc_final: 0.8240 (mm) REVERT: B 73 ASP cc_start: 0.6630 (p0) cc_final: 0.6369 (p0) REVERT: B 132 LYS cc_start: 0.8100 (mttm) cc_final: 0.7831 (mtmt) REVERT: B 303 MET cc_start: 0.8634 (mmm) cc_final: 0.8386 (mmm) REVERT: D 252 ILE cc_start: 0.9528 (mt) cc_final: 0.9296 (mt) REVERT: E 252 ILE cc_start: 0.9487 (mt) cc_final: 0.9246 (mt) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2677 time to fit residues: 123.7324 Evaluate side-chains 167 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 66 optimal weight: 0.0010 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 83 GLN B 54 ASN B 83 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 83 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13145 Z= 0.247 Angle : 0.861 10.903 17975 Z= 0.429 Chirality : 0.047 0.255 2130 Planarity : 0.005 0.040 2245 Dihedral : 7.829 59.109 2025 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.76 % Allowed : 9.92 % Favored : 87.32 % 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: -0.41 (0.19), residues: 1670 helix: 0.62 (0.21), residues: 525 sheet: 0.50 (0.25), residues: 380 loop : -1.31 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 255 HIS 0.002 0.001 HIS E 125 PHE 0.027 0.002 PHE B 115 TYR 0.023 0.002 TYR D 239 ARG 0.007 0.001 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7784 (ptmm) REVERT: A 204 ILE cc_start: 0.8672 (pt) cc_final: 0.8350 (mm) REVERT: A 222 LYS cc_start: 0.7588 (pttm) cc_final: 0.7382 (pttp) REVERT: B 156 MET cc_start: 0.7090 (ptp) cc_final: 0.6677 (mtm) REVERT: B 239 TYR cc_start: 0.8194 (m-80) cc_final: 0.7985 (m-80) REVERT: B 297 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7472 (mmmm) REVERT: B 303 MET cc_start: 0.8786 (mmm) cc_final: 0.8457 (mmm) REVERT: C 130 ASP cc_start: 0.7159 (t0) cc_final: 0.6948 (t0) REVERT: D 100 ASP cc_start: 0.7528 (m-30) cc_final: 0.7228 (t0) REVERT: D 130 ASP cc_start: 0.7007 (t0) cc_final: 0.6773 (t0) REVERT: D 302 TRP cc_start: 0.7966 (t60) cc_final: 0.7617 (t60) REVERT: D 303 MET cc_start: 0.8880 (mmm) cc_final: 0.8402 (mmp) REVERT: D 348 LEU cc_start: 0.9162 (mt) cc_final: 0.8867 (pp) REVERT: E 100 ASP cc_start: 0.7543 (m-30) cc_final: 0.6907 (t0) REVERT: E 279 MET cc_start: 0.8833 (mmm) cc_final: 0.8599 (mmm) REVERT: E 297 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7596 (mmmm) outliers start: 34 outliers final: 15 residues processed: 221 average time/residue: 0.2684 time to fit residues: 83.7634 Evaluate side-chains 168 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 297 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 162 optimal weight: 40.0000 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13145 Z= 0.315 Angle : 0.803 11.551 17975 Z= 0.398 Chirality : 0.045 0.241 2130 Planarity : 0.004 0.035 2245 Dihedral : 7.483 59.801 2025 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.93 % Allowed : 11.06 % Favored : 86.02 % 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: 0.10 (0.19), residues: 1670 helix: 1.62 (0.23), residues: 525 sheet: 0.30 (0.26), residues: 365 loop : -1.16 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 255 HIS 0.007 0.003 HIS B 217 PHE 0.035 0.002 PHE D 353 TYR 0.035 0.002 TYR A 238 ARG 0.005 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8819 (mmm) cc_final: 0.8298 (mmt) REVERT: C 72 MET cc_start: 0.7547 (tpp) cc_final: 0.7218 (tpp) REVERT: C 303 MET cc_start: 0.8813 (mmm) cc_final: 0.8478 (mmt) REVERT: D 100 ASP cc_start: 0.7639 (m-30) cc_final: 0.7179 (t0) REVERT: D 132 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7772 (mtmt) REVERT: D 302 TRP cc_start: 0.8067 (t-100) cc_final: 0.7657 (t60) REVERT: E 303 MET cc_start: 0.8835 (mmm) cc_final: 0.8631 (mmt) outliers start: 36 outliers final: 23 residues processed: 175 average time/residue: 0.2517 time to fit residues: 63.1048 Evaluate side-chains 144 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13145 Z= 0.291 Angle : 0.767 9.906 17975 Z= 0.378 Chirality : 0.044 0.234 2130 Planarity : 0.004 0.031 2245 Dihedral : 7.086 59.773 2025 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.93 % Allowed : 12.28 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1670 helix: 2.09 (0.23), residues: 530 sheet: 0.15 (0.26), residues: 375 loop : -0.95 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 255 HIS 0.004 0.002 HIS E 217 PHE 0.022 0.002 PHE D 353 TYR 0.023 0.002 TYR E 238 ARG 0.006 0.001 ARG C 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 TRP cc_start: 0.8054 (m-10) cc_final: 0.6891 (m-10) REVERT: E 72 MET cc_start: 0.7287 (tpp) cc_final: 0.6533 (tpp) REVERT: E 100 ASP cc_start: 0.7840 (m-30) cc_final: 0.7115 (t0) REVERT: E 302 TRP cc_start: 0.8382 (t-100) cc_final: 0.8094 (t60) outliers start: 36 outliers final: 26 residues processed: 162 average time/residue: 0.2465 time to fit residues: 58.2522 Evaluate side-chains 138 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13145 Z= 0.182 Angle : 0.738 14.038 17975 Z= 0.354 Chirality : 0.043 0.245 2130 Planarity : 0.003 0.035 2245 Dihedral : 6.703 59.888 2025 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.20 % Allowed : 13.90 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1670 helix: 2.17 (0.23), residues: 530 sheet: 0.06 (0.26), residues: 400 loop : -1.13 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 255 HIS 0.002 0.001 HIS E 217 PHE 0.018 0.001 PHE D 353 TYR 0.021 0.002 TYR E 144 ARG 0.003 0.001 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8849 (mmm) cc_final: 0.8156 (mmt) REVERT: B 100 ASP cc_start: 0.7626 (m-30) cc_final: 0.7072 (t0) REVERT: B 255 TRP cc_start: 0.7959 (m-10) cc_final: 0.6830 (m-10) REVERT: C 255 TRP cc_start: 0.7709 (m-10) cc_final: 0.6854 (m-10) REVERT: C 303 MET cc_start: 0.8772 (mmm) cc_final: 0.8327 (mmt) REVERT: D 179 MET cc_start: 0.8463 (mmm) cc_final: 0.8101 (mmm) REVERT: E 100 ASP cc_start: 0.7708 (m-30) cc_final: 0.7058 (t0) REVERT: E 302 TRP cc_start: 0.8318 (t-100) cc_final: 0.7814 (t60) REVERT: E 303 MET cc_start: 0.8818 (mmm) cc_final: 0.8571 (mmt) outliers start: 27 outliers final: 17 residues processed: 159 average time/residue: 0.2625 time to fit residues: 59.7873 Evaluate side-chains 138 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 181 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 132 optimal weight: 0.0770 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.0020 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13145 Z= 0.177 Angle : 0.726 10.156 17975 Z= 0.346 Chirality : 0.043 0.250 2130 Planarity : 0.003 0.035 2245 Dihedral : 6.476 59.929 2025 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.36 % Allowed : 14.31 % Favored : 83.33 % 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: 0.36 (0.20), residues: 1670 helix: 2.26 (0.22), residues: 530 sheet: 0.06 (0.25), residues: 400 loop : -1.20 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 255 HIS 0.003 0.001 HIS A 217 PHE 0.016 0.001 PHE D 353 TYR 0.038 0.002 TYR A 238 ARG 0.005 0.001 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7408 (m-30) cc_final: 0.7009 (t0) REVERT: B 255 TRP cc_start: 0.7942 (m-10) cc_final: 0.6808 (m-10) REVERT: B 303 MET cc_start: 0.8483 (mmm) cc_final: 0.8135 (tpt) REVERT: C 303 MET cc_start: 0.8796 (mmm) cc_final: 0.8247 (mmt) REVERT: D 303 MET cc_start: 0.8849 (mmm) cc_final: 0.8403 (mmt) REVERT: E 100 ASP cc_start: 0.7785 (m-30) cc_final: 0.7167 (t0) REVERT: E 303 MET cc_start: 0.8825 (mmm) cc_final: 0.8454 (mmt) outliers start: 29 outliers final: 20 residues processed: 158 average time/residue: 0.2482 time to fit residues: 56.7317 Evaluate side-chains 136 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 181 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13145 Z= 0.267 Angle : 0.753 9.643 17975 Z= 0.362 Chirality : 0.043 0.237 2130 Planarity : 0.004 0.038 2245 Dihedral : 6.620 59.548 2025 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.93 % Allowed : 14.72 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1670 helix: 2.49 (0.23), residues: 530 sheet: -0.12 (0.26), residues: 400 loop : -1.21 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 255 HIS 0.004 0.001 HIS B 231 PHE 0.016 0.001 PHE D 353 TYR 0.030 0.002 TYR A 238 ARG 0.004 0.001 ARG D 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 TRP cc_start: 0.7995 (m-10) cc_final: 0.6891 (m-10) REVERT: D 303 MET cc_start: 0.8907 (mmm) cc_final: 0.8438 (mmt) REVERT: D 348 LEU cc_start: 0.9201 (mm) cc_final: 0.8961 (pp) REVERT: E 100 ASP cc_start: 0.7730 (m-30) cc_final: 0.7118 (t0) REVERT: E 303 MET cc_start: 0.8801 (mmm) cc_final: 0.8429 (mmt) outliers start: 36 outliers final: 28 residues processed: 154 average time/residue: 0.2479 time to fit residues: 55.4141 Evaluate side-chains 137 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 0.0170 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 0.0670 chunk 144 optimal weight: 0.9980 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13145 Z= 0.184 Angle : 0.750 9.493 17975 Z= 0.357 Chirality : 0.043 0.239 2130 Planarity : 0.003 0.037 2245 Dihedral : 6.424 59.920 2025 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.11 % Allowed : 15.85 % Favored : 82.03 % 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: 0.44 (0.20), residues: 1670 helix: 2.47 (0.23), residues: 530 sheet: -0.02 (0.26), residues: 400 loop : -1.18 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 255 HIS 0.002 0.001 HIS A 217 PHE 0.014 0.001 PHE D 353 TYR 0.026 0.002 TYR A 238 ARG 0.003 0.001 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8816 (mmm) cc_final: 0.8239 (mmt) REVERT: B 255 TRP cc_start: 0.7951 (m-10) cc_final: 0.6819 (m-10) REVERT: B 303 MET cc_start: 0.8454 (mmm) cc_final: 0.8155 (tpt) REVERT: D 303 MET cc_start: 0.8808 (mmm) cc_final: 0.8272 (mmt) REVERT: D 348 LEU cc_start: 0.9191 (mm) cc_final: 0.8950 (pp) REVERT: E 100 ASP cc_start: 0.7754 (m-30) cc_final: 0.7162 (t0) REVERT: E 303 MET cc_start: 0.8800 (mmm) cc_final: 0.8463 (mmt) REVERT: E 307 LEU cc_start: 0.9397 (mt) cc_final: 0.9032 (pp) outliers start: 26 outliers final: 21 residues processed: 149 average time/residue: 0.2454 time to fit residues: 53.6907 Evaluate side-chains 135 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 181 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 64 optimal weight: 8.9990 chunk 116 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13145 Z= 0.219 Angle : 0.765 11.864 17975 Z= 0.365 Chirality : 0.043 0.235 2130 Planarity : 0.003 0.035 2245 Dihedral : 6.419 59.785 2025 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.28 % Allowed : 16.67 % Favored : 81.06 % 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: 0.46 (0.20), residues: 1670 helix: 2.44 (0.23), residues: 535 sheet: -0.03 (0.26), residues: 400 loop : -1.14 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 255 HIS 0.003 0.001 HIS E 231 PHE 0.014 0.001 PHE D 353 TYR 0.029 0.002 TYR D 238 ARG 0.003 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8797 (mmm) cc_final: 0.8219 (mmt) REVERT: B 255 TRP cc_start: 0.7978 (m-10) cc_final: 0.6831 (m-10) REVERT: B 303 MET cc_start: 0.8468 (mmm) cc_final: 0.8155 (tpt) REVERT: C 255 TRP cc_start: 0.7836 (m-10) cc_final: 0.7280 (m-10) REVERT: D 303 MET cc_start: 0.8778 (mmm) cc_final: 0.8216 (mmt) REVERT: D 348 LEU cc_start: 0.9199 (mm) cc_final: 0.8955 (pp) REVERT: E 100 ASP cc_start: 0.7765 (m-30) cc_final: 0.7198 (t0) REVERT: E 303 MET cc_start: 0.8804 (mmm) cc_final: 0.8498 (mmt) REVERT: E 307 LEU cc_start: 0.9445 (mt) cc_final: 0.9051 (pp) outliers start: 28 outliers final: 27 residues processed: 142 average time/residue: 0.2335 time to fit residues: 49.3240 Evaluate side-chains 140 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 181 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 0.0270 chunk 164 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 13 optimal weight: 0.0970 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13145 Z= 0.200 Angle : 0.776 11.872 17975 Z= 0.369 Chirality : 0.043 0.240 2130 Planarity : 0.003 0.035 2245 Dihedral : 6.341 59.900 2025 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.28 % Allowed : 16.91 % Favored : 80.81 % 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: 0.47 (0.20), residues: 1670 helix: 2.44 (0.22), residues: 535 sheet: 0.00 (0.26), residues: 400 loop : -1.15 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 255 HIS 0.002 0.001 HIS E 231 PHE 0.013 0.001 PHE D 353 TYR 0.025 0.002 TYR D 238 ARG 0.003 0.000 ARG D 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.8260 (mp0) cc_final: 0.7823 (mm-30) REVERT: A 303 MET cc_start: 0.8785 (mmm) cc_final: 0.8241 (mmt) REVERT: A 307 LEU cc_start: 0.9481 (mt) cc_final: 0.9099 (pp) REVERT: B 303 MET cc_start: 0.8494 (mmm) cc_final: 0.8180 (tpt) REVERT: C 255 TRP cc_start: 0.7828 (m-10) cc_final: 0.7277 (m-10) REVERT: C 303 MET cc_start: 0.8797 (mmm) cc_final: 0.8374 (mmt) REVERT: D 303 MET cc_start: 0.8776 (mmm) cc_final: 0.8132 (mmt) REVERT: D 348 LEU cc_start: 0.9200 (mm) cc_final: 0.8941 (pp) REVERT: E 100 ASP cc_start: 0.7731 (m-30) cc_final: 0.7136 (t0) REVERT: E 303 MET cc_start: 0.8782 (mmm) cc_final: 0.8441 (mmt) REVERT: E 307 LEU cc_start: 0.9451 (mt) cc_final: 0.9055 (pp) outliers start: 28 outliers final: 26 residues processed: 147 average time/residue: 0.2565 time to fit residues: 56.0744 Evaluate side-chains 142 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 181 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0370 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 54 optimal weight: 0.0030 chunk 134 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.6074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.034748 restraints weight = 90845.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.035637 restraints weight = 53653.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.036225 restraints weight = 37645.031| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13145 Z= 0.240 Angle : 0.795 12.661 17975 Z= 0.379 Chirality : 0.044 0.234 2130 Planarity : 0.004 0.039 2245 Dihedral : 6.376 59.429 2025 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.95 % Allowed : 17.80 % Favored : 80.24 % 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: 0.46 (0.21), residues: 1670 helix: 2.46 (0.22), residues: 565 sheet: -0.05 (0.26), residues: 400 loop : -1.31 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 255 HIS 0.003 0.001 HIS E 231 PHE 0.016 0.001 PHE E 116 TYR 0.029 0.002 TYR D 238 ARG 0.003 0.000 ARG D 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2208.37 seconds wall clock time: 41 minutes 16.42 seconds (2476.42 seconds total)