Starting phenix.real_space_refine on Mon Apr 8 18:01:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/04_2024/7u2n_26316_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/04_2024/7u2n_26316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/04_2024/7u2n_26316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/04_2024/7u2n_26316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/04_2024/7u2n_26316_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/04_2024/7u2n_26316_trim_updated.pdb" } resolution = 2.8 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= 0.005 sd= 2.345 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 105 5.16 5 C 9165 2.51 5 N 2255 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14080 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2771 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2771 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2771 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2771 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2771 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.67, per 1000 atoms: 0.54 Number of scatterers: 14080 At special positions: 0 Unit cell: (104.706, 106.368, 135.453, 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 105 16.00 O 2555 8.00 N 2255 7.00 C 9165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.03 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN D 54 " " NAG H 1 " - " ASN B 54 " " NAG I 1 " - " ASN C 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 25 sheets defined 35.9% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.840A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.937A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 removed outlier: 3.892A pdb=" N GLN A 242 " --> pdb=" O TYR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 4.197A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 287 removed outlier: 3.720A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.589A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 425 removed outlier: 3.564A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.162A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.841A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.937A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 242 removed outlier: 3.892A pdb=" N GLN D 242 " --> pdb=" O TYR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 removed outlier: 4.197A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 287 removed outlier: 3.721A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 324 removed outlier: 3.588A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 425 removed outlier: 3.564A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.161A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.841A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.937A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 removed outlier: 3.893A pdb=" N GLN B 242 " --> pdb=" O TYR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 4.197A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 287 removed outlier: 3.720A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 324 removed outlier: 3.588A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 425 removed outlier: 3.563A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.163A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.841A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.936A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 242 removed outlier: 3.892A pdb=" N GLN C 242 " --> pdb=" O TYR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 removed outlier: 4.197A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 287 removed outlier: 3.720A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 324 removed outlier: 3.590A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.564A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.162A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 removed outlier: 3.841A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.936A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.892A pdb=" N GLN E 242 " --> pdb=" O TYR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 256 removed outlier: 4.197A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 287 removed outlier: 3.719A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 324 removed outlier: 3.589A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 425 removed outlier: 3.564A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.162A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 removed outlier: 6.560A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.713A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= D, first strand: chain 'A' and resid 210 through 213 Processing sheet with id= E, first strand: chain 'A' and resid 216 through 218 Processing sheet with id= F, first strand: chain 'D' and resid 183 through 186 removed outlier: 6.560A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.713A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= I, first strand: chain 'D' and resid 210 through 213 Processing sheet with id= J, first strand: chain 'D' and resid 216 through 218 Processing sheet with id= K, first strand: chain 'B' and resid 183 through 186 removed outlier: 6.559A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.714A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= N, first strand: chain 'B' and resid 210 through 213 Processing sheet with id= O, first strand: chain 'B' and resid 216 through 218 Processing sheet with id= P, first strand: chain 'C' and resid 183 through 186 removed outlier: 6.560A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.713A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= S, first strand: chain 'C' and resid 210 through 213 Processing sheet with id= T, first strand: chain 'C' and resid 216 through 218 Processing sheet with id= U, first strand: chain 'E' and resid 183 through 186 removed outlier: 6.560A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.714A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= X, first strand: chain 'E' and resid 210 through 213 Processing sheet with id= Y, first strand: chain 'E' and resid 216 through 218 490 hydrogen bonds defined for protein. 1350 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: 3.82 Time building geometry restraints manager: 6.08 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: 4264 1.34 - 1.46: 3283 1.46 - 1.58: 6703 1.58 - 1.70: 0 1.70 - 1.82: 175 Bond restraints: 14425 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.90e+00 ... (remaining 14420 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.23: 439 106.23 - 113.20: 7879 113.20 - 120.17: 5288 120.17 - 127.15: 5836 127.15 - 134.12: 148 Bond angle restraints: 19590 Sorted by residual: angle pdb=" N ASN B 261 " pdb=" CA ASN B 261 " pdb=" CB ASN B 261 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N ASN E 261 " pdb=" CA ASN E 261 " pdb=" CB ASN E 261 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N ASN A 261 " pdb=" CA ASN A 261 " pdb=" CB ASN A 261 " ideal model delta sigma weight residual 114.17 109.94 4.23 1.14e+00 7.69e-01 1.38e+01 angle pdb=" O04 L2L C 600 " pdb=" S03 L2L C 600 " pdb=" O05 L2L C 600 " ideal model delta sigma weight residual 112.97 101.90 11.07 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N ASN D 261 " pdb=" CA ASN D 261 " pdb=" CB ASN D 261 " ideal model delta sigma weight residual 114.17 109.96 4.21 1.14e+00 7.69e-01 1.36e+01 ... (remaining 19585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8463 17.68 - 35.35: 252 35.35 - 53.02: 25 53.02 - 70.70: 0 70.70 - 88.37: 70 Dihedral angle restraints: 8810 sinusoidal: 3710 harmonic: 5100 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 41.46 51.54 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 41.49 51.51 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 41.50 51.50 1 1.00e+01 1.00e-02 3.62e+01 ... (remaining 8807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1784 0.052 - 0.104: 390 0.104 - 0.157: 71 0.157 - 0.209: 5 0.209 - 0.261: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2252 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 151 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C VAL C 151 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL C 151 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 152 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 151 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C VAL A 151 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 151 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 152 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 151 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.22e+00 pdb=" C VAL E 151 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL E 151 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU E 152 " 0.013 2.00e-02 2.50e+03 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1544 2.74 - 3.28: 14325 3.28 - 3.82: 22062 3.82 - 4.36: 28040 4.36 - 4.90: 46962 Nonbonded interactions: 112933 Sorted by model distance: nonbonded pdb=" O THR B 128 " pdb=" OG1 THR B 129 " model vdw 2.195 2.440 nonbonded pdb=" O THR C 128 " pdb=" OG1 THR C 129 " model vdw 2.195 2.440 nonbonded pdb=" OE2 GLU B 69 " pdb=" NH2 ARG B 234 " model vdw 2.195 2.520 nonbonded pdb=" OE2 GLU C 69 " pdb=" NH2 ARG C 234 " model vdw 2.196 2.520 nonbonded pdb=" O THR D 128 " pdb=" OG1 THR D 129 " model vdw 2.196 2.440 ... (remaining 112928 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 7.530 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 38.990 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.007 0.049 14425 Z= 0.475 Angle : 0.804 11.067 19590 Z= 0.431 Chirality : 0.048 0.261 2255 Planarity : 0.005 0.044 2420 Dihedral : 12.412 88.373 5470 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.18), residues: 1705 helix: -2.95 (0.19), residues: 535 sheet: -3.24 (0.22), residues: 370 loop : -2.33 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 259 HIS 0.004 0.001 HIS D 217 PHE 0.021 0.002 PHE A 115 TYR 0.012 0.002 TYR A 74 ARG 0.007 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7857 (tp30) cc_final: 0.7503 (tp30) REVERT: A 96 ASP cc_start: 0.7708 (m-30) cc_final: 0.7261 (m-30) REVERT: A 108 SER cc_start: 0.8592 (t) cc_final: 0.8309 (t) REVERT: A 126 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7204 (pm20) REVERT: A 130 ASP cc_start: 0.8395 (m-30) cc_final: 0.8132 (m-30) REVERT: A 132 LYS cc_start: 0.8163 (mttm) cc_final: 0.7951 (mtmp) REVERT: A 189 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8385 (ptpp) REVERT: A 206 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7979 (mttt) REVERT: A 312 SER cc_start: 0.8172 (m) cc_final: 0.7819 (p) REVERT: D 63 SER cc_start: 0.8337 (t) cc_final: 0.7751 (p) REVERT: D 75 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7468 (ttm-80) REVERT: D 96 ASP cc_start: 0.7877 (m-30) cc_final: 0.7503 (m-30) REVERT: D 102 ASP cc_start: 0.8025 (t0) cc_final: 0.7811 (t0) REVERT: D 108 SER cc_start: 0.8729 (t) cc_final: 0.8529 (t) REVERT: D 126 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6896 (pm20) REVERT: D 132 LYS cc_start: 0.8195 (mttm) cc_final: 0.7801 (mtmt) REVERT: D 189 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8364 (ptpp) REVERT: D 206 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7877 (mttm) REVERT: D 210 ASP cc_start: 0.8283 (m-30) cc_final: 0.7988 (m-30) REVERT: D 235 GLN cc_start: 0.8053 (mm110) cc_final: 0.7747 (mt0) REVERT: D 312 SER cc_start: 0.8196 (m) cc_final: 0.7911 (p) REVERT: B 28 GLU cc_start: 0.7877 (tp30) cc_final: 0.7590 (tp30) REVERT: B 31 ASP cc_start: 0.8304 (m-30) cc_final: 0.7894 (m-30) REVERT: B 96 ASP cc_start: 0.7720 (m-30) cc_final: 0.7142 (m-30) REVERT: B 108 SER cc_start: 0.8576 (t) cc_final: 0.8365 (t) REVERT: B 126 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7174 (pm20) REVERT: B 132 LYS cc_start: 0.8143 (mttm) cc_final: 0.7866 (mtmp) REVERT: B 206 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7992 (mttm) REVERT: B 210 ASP cc_start: 0.8300 (m-30) cc_final: 0.8058 (m-30) REVERT: B 312 SER cc_start: 0.8159 (m) cc_final: 0.7845 (p) REVERT: C 28 GLU cc_start: 0.7845 (tp30) cc_final: 0.7550 (tp30) REVERT: C 96 ASP cc_start: 0.7756 (m-30) cc_final: 0.7356 (m-30) REVERT: C 108 SER cc_start: 0.8746 (t) cc_final: 0.8505 (t) REVERT: C 126 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7106 (pm20) REVERT: C 130 ASP cc_start: 0.8482 (m-30) cc_final: 0.8176 (m-30) REVERT: C 132 LYS cc_start: 0.8216 (mttm) cc_final: 0.7936 (mtmp) REVERT: C 189 LYS cc_start: 0.8559 (ptpt) cc_final: 0.8290 (ptpp) REVERT: C 206 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7994 (mttm) REVERT: C 210 ASP cc_start: 0.8236 (m-30) cc_final: 0.7909 (m-30) REVERT: C 229 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7462 (mmm-85) REVERT: C 235 GLN cc_start: 0.7989 (mm110) cc_final: 0.7673 (mt0) REVERT: C 312 SER cc_start: 0.8218 (m) cc_final: 0.7936 (p) REVERT: E 28 GLU cc_start: 0.7947 (tp30) cc_final: 0.7647 (tp30) REVERT: E 75 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: E 96 ASP cc_start: 0.7711 (m-30) cc_final: 0.7202 (m-30) REVERT: E 108 SER cc_start: 0.8681 (t) cc_final: 0.8388 (t) REVERT: E 126 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7224 (pm20) REVERT: E 132 LYS cc_start: 0.8127 (mttm) cc_final: 0.7844 (mtmp) REVERT: E 189 LYS cc_start: 0.8466 (ptpt) cc_final: 0.8238 (ptpp) REVERT: E 210 ASP cc_start: 0.8281 (m-30) cc_final: 0.7933 (m-30) REVERT: E 235 GLN cc_start: 0.8057 (mm110) cc_final: 0.7851 (mm110) REVERT: E 312 SER cc_start: 0.8193 (m) cc_final: 0.7910 (p) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 1.1358 time to fit residues: 603.8393 Evaluate side-chains 379 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 77 ASN A 82 GLN A 141 ASN A 202 GLN A 231 HIS A 282 GLN D 77 ASN D 82 GLN D 141 ASN D 231 HIS D 282 GLN D 418 ASN B 62 ASN B 77 ASN B 82 GLN B 141 ASN B 219 ASN B 231 HIS B 282 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 77 ASN C 82 GLN C 141 ASN C 219 ASN C 231 HIS C 282 GLN E 62 ASN E 77 ASN E 82 GLN E 141 ASN E 171 GLN E 231 HIS E 282 GLN ** E 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14425 Z= 0.257 Angle : 0.723 5.565 19590 Z= 0.374 Chirality : 0.048 0.169 2255 Planarity : 0.006 0.060 2420 Dihedral : 12.319 75.490 2190 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.77 % Allowed : 13.73 % Favored : 83.50 % 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: -2.82 (0.19), residues: 1705 helix: -1.46 (0.21), residues: 535 sheet: -2.61 (0.23), residues: 370 loop : -1.63 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 259 HIS 0.004 0.001 HIS A 231 PHE 0.025 0.002 PHE D 414 TYR 0.015 0.002 TYR A 425 ARG 0.014 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 389 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 104 SER cc_start: 0.8516 (t) cc_final: 0.7914 (p) REVERT: A 126 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7260 (pm20) REVERT: A 141 ASN cc_start: 0.8319 (m110) cc_final: 0.8027 (m110) REVERT: A 189 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8301 (ptmm) REVERT: A 235 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: D 49 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8766 (mmmm) REVERT: D 63 SER cc_start: 0.8403 (t) cc_final: 0.7838 (p) REVERT: D 75 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7518 (ttm-80) REVERT: D 96 ASP cc_start: 0.7674 (m-30) cc_final: 0.7275 (m-30) REVERT: D 126 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6826 (pm20) REVERT: D 132 LYS cc_start: 0.8037 (mttm) cc_final: 0.7705 (mtmt) REVERT: D 135 ARG cc_start: 0.7914 (ptp-170) cc_final: 0.7655 (ptp-170) REVERT: D 141 ASN cc_start: 0.8195 (m110) cc_final: 0.7796 (m110) REVERT: D 179 MET cc_start: 0.8090 (mmm) cc_final: 0.7853 (mmm) REVERT: D 189 LYS cc_start: 0.8446 (ptpt) cc_final: 0.8244 (ptpp) REVERT: D 206 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7788 (mttm) REVERT: D 210 ASP cc_start: 0.8023 (m-30) cc_final: 0.7697 (m-30) REVERT: D 227 GLU cc_start: 0.8120 (pt0) cc_final: 0.7705 (pt0) REVERT: D 235 GLN cc_start: 0.7948 (mm110) cc_final: 0.7703 (mt0) REVERT: D 262 MET cc_start: 0.8214 (mpp) cc_final: 0.7069 (tmt) REVERT: B 31 ASP cc_start: 0.8341 (m-30) cc_final: 0.7942 (m-30) REVERT: B 126 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7126 (pm20) REVERT: B 132 LYS cc_start: 0.8034 (mttm) cc_final: 0.7830 (mtmp) REVERT: B 179 MET cc_start: 0.8106 (mmm) cc_final: 0.7702 (mmm) REVERT: B 206 LYS cc_start: 0.8291 (mtpt) cc_final: 0.8023 (mttt) REVERT: B 219 ASN cc_start: 0.8336 (p0) cc_final: 0.8064 (p0) REVERT: B 235 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: B 262 MET cc_start: 0.8013 (mpp) cc_final: 0.6976 (tmt) REVERT: C 94 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7160 (t80) REVERT: C 96 ASP cc_start: 0.7542 (m-30) cc_final: 0.7144 (m-30) REVERT: C 126 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6984 (pm20) REVERT: C 130 ASP cc_start: 0.8435 (m-30) cc_final: 0.8228 (m-30) REVERT: C 189 LYS cc_start: 0.8482 (ptpt) cc_final: 0.8201 (ptpp) REVERT: C 206 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7897 (mttm) REVERT: C 210 ASP cc_start: 0.7917 (m-30) cc_final: 0.7548 (m-30) REVERT: C 235 GLN cc_start: 0.7998 (mm110) cc_final: 0.7754 (mt0) REVERT: C 401 ARG cc_start: 0.8675 (mmm160) cc_final: 0.8328 (mmm-85) REVERT: E 28 GLU cc_start: 0.7882 (tp30) cc_final: 0.7641 (tp30) REVERT: E 69 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7996 (mt-10) REVERT: E 75 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7608 (ttm-80) REVERT: E 126 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6921 (pm20) REVERT: E 132 LYS cc_start: 0.8022 (mttm) cc_final: 0.7799 (mtmp) REVERT: E 189 LYS cc_start: 0.8377 (ptpt) cc_final: 0.8143 (ptpp) REVERT: E 210 ASP cc_start: 0.7962 (m-30) cc_final: 0.7709 (m-30) REVERT: E 235 GLN cc_start: 0.7979 (mm110) cc_final: 0.7574 (mt0) REVERT: E 262 MET cc_start: 0.8249 (mpp) cc_final: 0.7172 (tmt) outliers start: 42 outliers final: 16 residues processed: 399 average time/residue: 1.1601 time to fit residues: 510.1608 Evaluate side-chains 358 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 339 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 424 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 202 GLN B 321 ASN B 418 ASN C 282 GLN ** E 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14425 Z= 0.206 Angle : 0.633 6.437 19590 Z= 0.329 Chirality : 0.044 0.138 2255 Planarity : 0.005 0.059 2420 Dihedral : 11.115 64.203 2190 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.89 % Allowed : 17.62 % Favored : 78.48 % 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: -2.01 (0.20), residues: 1705 helix: -0.49 (0.22), residues: 555 sheet: -2.13 (0.24), residues: 370 loop : -1.42 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 259 HIS 0.002 0.001 HIS A 231 PHE 0.017 0.001 PHE E 414 TYR 0.018 0.002 TYR A 317 ARG 0.005 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 368 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8113 (mt-10) REVERT: A 104 SER cc_start: 0.8418 (t) cc_final: 0.7870 (p) REVERT: A 126 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7228 (pm20) REVERT: A 130 ASP cc_start: 0.8446 (m-30) cc_final: 0.8156 (m-30) REVERT: A 141 ASN cc_start: 0.8219 (m110) cc_final: 0.7885 (m110) REVERT: D 43 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8317 (mtm180) REVERT: D 49 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8699 (mmmm) REVERT: D 75 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7474 (ttm-80) REVERT: D 126 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6823 (pm20) REVERT: D 132 LYS cc_start: 0.7965 (mttm) cc_final: 0.7649 (mtmt) REVERT: D 189 LYS cc_start: 0.8398 (ptpt) cc_final: 0.8188 (ptpp) REVERT: D 206 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7791 (mttm) REVERT: D 210 ASP cc_start: 0.8021 (m-30) cc_final: 0.7675 (m-30) REVERT: D 212 ARG cc_start: 0.7616 (pmm-80) cc_final: 0.6966 (ptt90) REVERT: D 227 GLU cc_start: 0.8158 (pt0) cc_final: 0.7742 (pt0) REVERT: D 235 GLN cc_start: 0.7881 (mm110) cc_final: 0.7638 (mt0) REVERT: D 262 MET cc_start: 0.7852 (mpp) cc_final: 0.6814 (tmt) REVERT: B 100 ASP cc_start: 0.8019 (m-30) cc_final: 0.7305 (t70) REVERT: B 126 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7058 (pm20) REVERT: B 179 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7742 (mmm) REVERT: B 206 LYS cc_start: 0.8285 (mtpt) cc_final: 0.8053 (mttp) REVERT: B 235 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: B 262 MET cc_start: 0.7696 (mpp) cc_final: 0.6689 (tmt) REVERT: C 43 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8259 (mtm180) REVERT: C 94 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7124 (t80) REVERT: C 96 ASP cc_start: 0.7398 (m-30) cc_final: 0.7116 (m-30) REVERT: C 126 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6986 (pm20) REVERT: C 206 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7896 (mttm) REVERT: C 229 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7302 (mmm-85) REVERT: C 235 GLN cc_start: 0.7921 (mm110) cc_final: 0.7694 (mt0) REVERT: C 243 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7837 (mtt) REVERT: C 401 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8308 (mmm-85) REVERT: E 28 GLU cc_start: 0.7860 (tp30) cc_final: 0.7588 (tp30) REVERT: E 69 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8113 (mt-10) REVERT: E 71 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9121 (p) REVERT: E 75 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7618 (ttm-80) REVERT: E 102 ASP cc_start: 0.7731 (t70) cc_final: 0.7476 (t0) REVERT: E 126 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6916 (pm20) REVERT: E 132 LYS cc_start: 0.7953 (mttm) cc_final: 0.7717 (mtmp) REVERT: E 210 ASP cc_start: 0.8048 (m-30) cc_final: 0.7743 (m-30) REVERT: E 235 GLN cc_start: 0.7962 (mm110) cc_final: 0.7601 (mt0) REVERT: E 262 MET cc_start: 0.7866 (mpp) cc_final: 0.6906 (tmt) outliers start: 59 outliers final: 25 residues processed: 386 average time/residue: 1.1898 time to fit residues: 506.0544 Evaluate side-chains 364 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 334 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.0000 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN D 282 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN C 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14425 Z= 0.187 Angle : 0.623 6.999 19590 Z= 0.318 Chirality : 0.044 0.139 2255 Planarity : 0.004 0.055 2420 Dihedral : 9.615 54.893 2190 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.83 % Allowed : 20.13 % Favored : 76.04 % 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: -1.47 (0.20), residues: 1705 helix: 0.09 (0.23), residues: 555 sheet: -1.67 (0.25), residues: 370 loop : -1.30 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 259 HIS 0.001 0.000 HIS C 125 PHE 0.017 0.001 PHE D 414 TYR 0.016 0.001 TYR C 317 ARG 0.003 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 333 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8325 (mtm180) REVERT: A 49 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8675 (mmmm) REVERT: A 94 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 126 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7211 (pm20) REVERT: A 135 ARG cc_start: 0.7902 (ptp-170) cc_final: 0.7535 (ptp-170) REVERT: A 141 ASN cc_start: 0.8199 (m110) cc_final: 0.7851 (m110) REVERT: A 235 GLN cc_start: 0.8252 (mm110) cc_final: 0.7584 (mt0) REVERT: A 243 MET cc_start: 0.8022 (mpp) cc_final: 0.7621 (mtt) REVERT: D 43 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8309 (mtm180) REVERT: D 49 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8647 (mmmm) REVERT: D 63 SER cc_start: 0.8453 (t) cc_final: 0.8050 (p) REVERT: D 75 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7441 (ttm-80) REVERT: D 94 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8103 (t80) REVERT: D 105 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6091 (mpp) REVERT: D 126 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6802 (pm20) REVERT: D 132 LYS cc_start: 0.7938 (mttm) cc_final: 0.7612 (mtmt) REVERT: D 179 MET cc_start: 0.8111 (mmm) cc_final: 0.7904 (mmm) REVERT: D 210 ASP cc_start: 0.8033 (m-30) cc_final: 0.7695 (m-30) REVERT: D 227 GLU cc_start: 0.8127 (pt0) cc_final: 0.7781 (pt0) REVERT: D 235 GLN cc_start: 0.7869 (mm110) cc_final: 0.7519 (mt0) REVERT: D 262 MET cc_start: 0.7507 (mpp) cc_final: 0.6706 (tmt) REVERT: B 126 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7108 (pm20) REVERT: B 179 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7843 (mmm) REVERT: B 206 LYS cc_start: 0.8251 (mtpt) cc_final: 0.8045 (mttp) REVERT: B 235 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: B 262 MET cc_start: 0.7453 (mpp) cc_final: 0.6741 (tmt) REVERT: C 43 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8331 (mtm180) REVERT: C 94 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7123 (t80) REVERT: C 96 ASP cc_start: 0.7305 (m-30) cc_final: 0.7080 (m-30) REVERT: C 126 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6857 (pm20) REVERT: C 229 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7367 (mmm-85) REVERT: C 235 GLN cc_start: 0.7989 (mm110) cc_final: 0.7713 (mt0) REVERT: C 243 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7527 (mtt) REVERT: C 279 MET cc_start: 0.8727 (tpp) cc_final: 0.7084 (mpp) REVERT: C 401 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8296 (mmm-85) REVERT: E 75 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7611 (ttm-80) REVERT: E 126 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6920 (pm20) REVERT: E 132 LYS cc_start: 0.7983 (mttm) cc_final: 0.7752 (mtmp) REVERT: E 138 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8671 (mtmt) REVERT: E 206 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7733 (mttt) REVERT: E 210 ASP cc_start: 0.8057 (m-30) cc_final: 0.7735 (m-30) REVERT: E 219 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.8009 (p0) REVERT: E 235 GLN cc_start: 0.7951 (mm110) cc_final: 0.7618 (mt0) REVERT: E 262 MET cc_start: 0.7440 (mpp) cc_final: 0.6789 (tmt) outliers start: 58 outliers final: 23 residues processed: 353 average time/residue: 1.2081 time to fit residues: 469.4800 Evaluate side-chains 332 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 300 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 219 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN D 131 ASN D 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 14425 Z= 0.372 Angle : 0.689 7.967 19590 Z= 0.356 Chirality : 0.046 0.141 2255 Planarity : 0.005 0.053 2420 Dihedral : 8.674 45.912 2190 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.94 % Allowed : 18.61 % Favored : 75.45 % 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: -1.23 (0.20), residues: 1705 helix: 0.49 (0.24), residues: 545 sheet: -1.61 (0.26), residues: 370 loop : -1.26 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 259 HIS 0.003 0.001 HIS A 125 PHE 0.016 0.002 PHE E 124 TYR 0.015 0.002 TYR A 317 ARG 0.005 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 302 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.7421 (t80) REVERT: A 141 ASN cc_start: 0.8274 (m110) cc_final: 0.7947 (m110) REVERT: A 243 MET cc_start: 0.8223 (mpp) cc_final: 0.7562 (mtt) REVERT: A 312 SER cc_start: 0.8011 (OUTLIER) cc_final: 0.7607 (p) REVERT: A 391 MET cc_start: 0.4965 (pmm) cc_final: 0.4761 (pmm) REVERT: D 75 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7523 (ttm-80) REVERT: D 81 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7198 (mpp-170) REVERT: D 94 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7928 (t80) REVERT: D 126 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6881 (pm20) REVERT: D 206 LYS cc_start: 0.8254 (mttp) cc_final: 0.7879 (mttp) REVERT: D 210 ASP cc_start: 0.8067 (m-30) cc_final: 0.7636 (m-30) REVERT: D 227 GLU cc_start: 0.8204 (pt0) cc_final: 0.7892 (pt0) REVERT: D 235 GLN cc_start: 0.8058 (mm110) cc_final: 0.7807 (mt0) REVERT: D 243 MET cc_start: 0.8272 (tpp) cc_final: 0.7547 (mtt) REVERT: D 262 MET cc_start: 0.7392 (mpp) cc_final: 0.6797 (tmt) REVERT: B 28 GLU cc_start: 0.7879 (tp30) cc_final: 0.7489 (tp30) REVERT: B 126 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7179 (pm20) REVERT: B 179 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7812 (mmt) REVERT: B 206 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8119 (mttt) REVERT: B 219 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7982 (p0) REVERT: B 235 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: B 262 MET cc_start: 0.7215 (mpp) cc_final: 0.6670 (tmt) REVERT: C 94 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7463 (t80) REVERT: C 96 ASP cc_start: 0.7313 (m-30) cc_final: 0.6980 (m-30) REVERT: C 126 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7008 (pm20) REVERT: C 189 LYS cc_start: 0.8461 (ptpp) cc_final: 0.7982 (ptpp) REVERT: C 219 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7970 (p0) REVERT: C 235 GLN cc_start: 0.8167 (mm110) cc_final: 0.7931 (mt0) REVERT: C 243 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7771 (mtt) REVERT: C 312 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7590 (p) REVERT: C 401 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8303 (mmm-85) REVERT: E 75 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7637 (ttm-80) REVERT: E 93 GLU cc_start: 0.8896 (pp20) cc_final: 0.8611 (pp20) REVERT: E 126 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7120 (pm20) REVERT: E 132 LYS cc_start: 0.8022 (mttm) cc_final: 0.7773 (mtmp) REVERT: E 138 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8668 (mtmt) REVERT: E 206 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7845 (mttt) REVERT: E 210 ASP cc_start: 0.8083 (m-30) cc_final: 0.7646 (m-30) REVERT: E 219 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7619 (p0) REVERT: E 235 GLN cc_start: 0.8123 (mm110) cc_final: 0.7768 (mt0) REVERT: E 262 MET cc_start: 0.7468 (mpp) cc_final: 0.6817 (tmt) REVERT: E 284 SER cc_start: 0.9255 (p) cc_final: 0.9050 (p) REVERT: E 312 SER cc_start: 0.8055 (OUTLIER) cc_final: 0.7661 (p) outliers start: 90 outliers final: 43 residues processed: 335 average time/residue: 1.1990 time to fit residues: 442.2461 Evaluate side-chains 345 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 288 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 282 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14425 Z= 0.224 Angle : 0.635 8.021 19590 Z= 0.323 Chirality : 0.044 0.151 2255 Planarity : 0.004 0.049 2420 Dihedral : 7.003 32.705 2190 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.29 % Allowed : 21.32 % Favored : 74.39 % 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: -0.95 (0.21), residues: 1705 helix: 0.71 (0.24), residues: 550 sheet: -1.42 (0.26), residues: 370 loop : -1.12 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 186 HIS 0.002 0.001 HIS C 217 PHE 0.018 0.001 PHE A 29 TYR 0.013 0.001 TYR A 317 ARG 0.004 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 308 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7419 (t80) REVERT: A 135 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7526 (ptp-170) REVERT: A 141 ASN cc_start: 0.8205 (m110) cc_final: 0.7879 (m110) REVERT: A 235 GLN cc_start: 0.8360 (mt0) cc_final: 0.7707 (mt0) REVERT: A 243 MET cc_start: 0.8177 (tpp) cc_final: 0.7474 (mtt) REVERT: A 312 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7588 (p) REVERT: A 391 MET cc_start: 0.5169 (pmm) cc_final: 0.4651 (pmm) REVERT: D 75 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7470 (ttm-80) REVERT: D 126 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6774 (pm20) REVERT: D 206 LYS cc_start: 0.8212 (mttp) cc_final: 0.7941 (mttp) REVERT: D 210 ASP cc_start: 0.8037 (m-30) cc_final: 0.7619 (m-30) REVERT: D 227 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: D 243 MET cc_start: 0.8234 (tpp) cc_final: 0.7618 (mtt) REVERT: D 262 MET cc_start: 0.7245 (mpp) cc_final: 0.6796 (tmt) REVERT: B 126 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7111 (pm20) REVERT: B 179 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7804 (mmt) REVERT: B 206 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8082 (mttt) REVERT: B 219 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7876 (p0) REVERT: B 235 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7973 (mt0) REVERT: B 262 MET cc_start: 0.7187 (mpp) cc_final: 0.6758 (tmt) REVERT: C 94 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7312 (t80) REVERT: C 96 ASP cc_start: 0.7218 (m-30) cc_final: 0.6960 (m-30) REVERT: C 126 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6926 (pm20) REVERT: C 229 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7662 (mtt-85) REVERT: C 235 GLN cc_start: 0.8035 (mm110) cc_final: 0.7823 (mt0) REVERT: C 243 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7657 (mtt) REVERT: C 401 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8298 (mmm-85) REVERT: E 75 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7554 (ttm-80) REVERT: E 94 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7883 (t80) REVERT: E 120 LYS cc_start: 0.8283 (tttp) cc_final: 0.8026 (tttt) REVERT: E 126 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6901 (pm20) REVERT: E 132 LYS cc_start: 0.7968 (mttm) cc_final: 0.7732 (mtmp) REVERT: E 210 ASP cc_start: 0.8071 (m-30) cc_final: 0.7655 (m-30) REVERT: E 235 GLN cc_start: 0.8012 (mm110) cc_final: 0.7656 (mt0) REVERT: E 262 MET cc_start: 0.7213 (mpp) cc_final: 0.6775 (tmt) REVERT: E 312 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7643 (p) outliers start: 65 outliers final: 34 residues processed: 329 average time/residue: 1.2496 time to fit residues: 452.0796 Evaluate side-chains 332 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 288 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 ASN D 282 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14425 Z= 0.201 Angle : 0.638 8.846 19590 Z= 0.324 Chirality : 0.044 0.143 2255 Planarity : 0.004 0.046 2420 Dihedral : 5.779 28.119 2190 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.16 % Allowed : 21.65 % Favored : 74.19 % 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: -0.90 (0.21), residues: 1705 helix: 0.85 (0.24), residues: 550 sheet: -1.56 (0.25), residues: 395 loop : -1.03 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 422 HIS 0.001 0.000 HIS C 217 PHE 0.018 0.001 PHE A 29 TYR 0.013 0.001 TYR A 317 ARG 0.006 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 292 time to evaluate : 2.440 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 94 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.7360 (t80) REVERT: A 141 ASN cc_start: 0.8198 (m110) cc_final: 0.7884 (m110) REVERT: A 235 GLN cc_start: 0.8362 (mt0) cc_final: 0.7726 (mt0) REVERT: A 243 MET cc_start: 0.8163 (tpp) cc_final: 0.7576 (mtt) REVERT: A 312 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7624 (p) REVERT: A 391 MET cc_start: 0.5127 (pmm) cc_final: 0.4567 (pmm) REVERT: D 75 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7451 (ttm-80) REVERT: D 94 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7684 (t80) REVERT: D 126 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6767 (pm20) REVERT: D 206 LYS cc_start: 0.8215 (mttp) cc_final: 0.7969 (mttp) REVERT: D 210 ASP cc_start: 0.8040 (m-30) cc_final: 0.7636 (m-30) REVERT: D 227 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: D 243 MET cc_start: 0.8243 (tpp) cc_final: 0.7594 (mtt) REVERT: D 262 MET cc_start: 0.7015 (mpp) cc_final: 0.6756 (tmt) REVERT: B 34 MET cc_start: 0.5482 (OUTLIER) cc_final: 0.5101 (mpp) REVERT: B 126 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7096 (pm20) REVERT: B 179 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7793 (mmt) REVERT: B 189 LYS cc_start: 0.8184 (ptpp) cc_final: 0.7851 (ptpp) REVERT: B 235 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: B 262 MET cc_start: 0.7001 (mpp) cc_final: 0.6687 (tmt) REVERT: C 94 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7240 (t80) REVERT: C 126 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6919 (pm20) REVERT: C 227 GLU cc_start: 0.8176 (pt0) cc_final: 0.7948 (pt0) REVERT: C 235 GLN cc_start: 0.8000 (mm110) cc_final: 0.7784 (mt0) REVERT: C 243 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7676 (mtt) REVERT: C 279 MET cc_start: 0.8703 (tpp) cc_final: 0.7022 (mpp) REVERT: C 312 SER cc_start: 0.7956 (m) cc_final: 0.7615 (p) REVERT: C 401 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8290 (mmm-85) REVERT: E 75 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7523 (ttm-80) REVERT: E 94 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7652 (t80) REVERT: E 120 LYS cc_start: 0.8313 (tttp) cc_final: 0.8068 (tttt) REVERT: E 126 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6869 (pm20) REVERT: E 132 LYS cc_start: 0.7955 (mttm) cc_final: 0.7728 (mtmp) REVERT: E 138 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8524 (ttpp) REVERT: E 206 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7773 (mttm) REVERT: E 210 ASP cc_start: 0.8052 (m-30) cc_final: 0.7630 (m-30) REVERT: E 235 GLN cc_start: 0.7990 (mm110) cc_final: 0.7625 (mt0) REVERT: E 262 MET cc_start: 0.7033 (mpp) cc_final: 0.6766 (tmt) REVERT: E 312 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7658 (p) outliers start: 63 outliers final: 40 residues processed: 319 average time/residue: 1.0670 time to fit residues: 374.9411 Evaluate side-chains 335 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 284 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 8.9990 chunk 97 optimal weight: 0.0470 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 282 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14425 Z= 0.225 Angle : 0.640 9.699 19590 Z= 0.323 Chirality : 0.044 0.141 2255 Planarity : 0.004 0.041 2420 Dihedral : 5.073 24.542 2190 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.42 % Allowed : 21.32 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1705 helix: 1.03 (0.24), residues: 550 sheet: -1.51 (0.25), residues: 395 loop : -1.07 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.001 0.000 HIS D 217 PHE 0.016 0.001 PHE A 29 TYR 0.014 0.001 TYR B 317 ARG 0.007 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 293 time to evaluate : 1.659 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 94 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.7204 (t80) REVERT: A 243 MET cc_start: 0.8234 (tpp) cc_final: 0.7605 (mtt) REVERT: A 312 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7563 (p) REVERT: A 391 MET cc_start: 0.5167 (pmm) cc_final: 0.4563 (pmm) REVERT: D 75 ARG cc_start: 0.7796 (ttm-80) cc_final: 0.7435 (ttm-80) REVERT: D 94 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.7547 (t80) REVERT: D 126 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6771 (pm20) REVERT: D 206 LYS cc_start: 0.8246 (mttp) cc_final: 0.7995 (mttp) REVERT: D 210 ASP cc_start: 0.8031 (m-30) cc_final: 0.7632 (m-30) REVERT: D 227 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: D 262 MET cc_start: 0.6922 (mpp) cc_final: 0.6623 (tmt) REVERT: B 126 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7107 (pm20) REVERT: B 179 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7792 (mmt) REVERT: B 189 LYS cc_start: 0.8018 (ptpp) cc_final: 0.7657 (ptpp) REVERT: B 206 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8045 (mttm) REVERT: B 235 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: B 262 MET cc_start: 0.6873 (mpp) cc_final: 0.6669 (tmt) REVERT: C 94 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7270 (t80) REVERT: C 126 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6945 (pm20) REVERT: C 227 GLU cc_start: 0.8199 (pt0) cc_final: 0.7973 (pt0) REVERT: C 229 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7839 (mtp-110) REVERT: C 235 GLN cc_start: 0.8027 (mm110) cc_final: 0.7789 (mt0) REVERT: C 243 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7728 (mtt) REVERT: C 279 MET cc_start: 0.8704 (tpp) cc_final: 0.7102 (mpp) REVERT: C 312 SER cc_start: 0.7950 (OUTLIER) cc_final: 0.7611 (p) REVERT: C 401 ARG cc_start: 0.8676 (mmm160) cc_final: 0.8289 (mmm-85) REVERT: E 75 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7509 (ttm-80) REVERT: E 94 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7629 (t80) REVERT: E 120 LYS cc_start: 0.8319 (tttp) cc_final: 0.8068 (tttt) REVERT: E 126 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6890 (pm20) REVERT: E 132 LYS cc_start: 0.7972 (mttm) cc_final: 0.7735 (mtmp) REVERT: E 206 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7791 (mttm) REVERT: E 210 ASP cc_start: 0.8071 (m-30) cc_final: 0.7654 (m-30) REVERT: E 235 GLN cc_start: 0.8011 (mm110) cc_final: 0.7663 (mt0) REVERT: E 312 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7649 (p) outliers start: 67 outliers final: 40 residues processed: 323 average time/residue: 1.1784 time to fit residues: 419.1815 Evaluate side-chains 339 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 288 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 282 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14425 Z= 0.203 Angle : 0.638 12.248 19590 Z= 0.320 Chirality : 0.044 0.142 2255 Planarity : 0.004 0.039 2420 Dihedral : 4.808 26.170 2190 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.09 % Allowed : 21.85 % Favored : 74.06 % 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: -0.71 (0.21), residues: 1705 helix: 1.15 (0.24), residues: 550 sheet: -1.41 (0.25), residues: 390 loop : -1.09 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 259 HIS 0.001 0.000 HIS C 217 PHE 0.014 0.001 PHE C 322 TYR 0.013 0.001 TYR D 317 ARG 0.008 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 289 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7246 (t80) REVERT: A 243 MET cc_start: 0.8211 (tpp) cc_final: 0.7600 (mtt) REVERT: A 312 SER cc_start: 0.7954 (OUTLIER) cc_final: 0.7533 (p) REVERT: A 391 MET cc_start: 0.5003 (pmm) cc_final: 0.4402 (pmm) REVERT: D 75 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7433 (ttm-80) REVERT: D 94 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7451 (t80) REVERT: D 126 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6709 (pm20) REVERT: D 206 LYS cc_start: 0.8227 (mttp) cc_final: 0.7988 (mttp) REVERT: D 210 ASP cc_start: 0.8006 (m-30) cc_final: 0.7601 (m-30) REVERT: D 227 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: D 262 MET cc_start: 0.7002 (mpp) cc_final: 0.6693 (tmt) REVERT: B 126 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7077 (pm20) REVERT: B 179 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7810 (mmt) REVERT: B 189 LYS cc_start: 0.7927 (ptpp) cc_final: 0.7583 (ptpp) REVERT: B 206 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8034 (mttm) REVERT: B 219 ASN cc_start: 0.8147 (p0) cc_final: 0.7813 (p0) REVERT: B 235 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: C 94 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7164 (t80) REVERT: C 126 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6882 (pm20) REVERT: C 229 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7821 (mtp-110) REVERT: C 235 GLN cc_start: 0.8103 (mm110) cc_final: 0.7812 (mt0) REVERT: C 243 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7739 (mtt) REVERT: C 279 MET cc_start: 0.8700 (tpp) cc_final: 0.7103 (mpp) REVERT: C 312 SER cc_start: 0.7955 (m) cc_final: 0.7605 (p) REVERT: C 401 ARG cc_start: 0.8678 (mmm160) cc_final: 0.8276 (mmm-85) REVERT: E 75 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7524 (ttm-80) REVERT: E 94 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7460 (t80) REVERT: E 120 LYS cc_start: 0.8304 (tttp) cc_final: 0.8054 (tttt) REVERT: E 126 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6881 (pm20) REVERT: E 132 LYS cc_start: 0.7961 (mttm) cc_final: 0.7727 (mtmp) REVERT: E 138 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8698 (tttt) REVERT: E 206 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7790 (mttm) REVERT: E 210 ASP cc_start: 0.8074 (m-30) cc_final: 0.7631 (m-30) REVERT: E 235 GLN cc_start: 0.7976 (mm110) cc_final: 0.7624 (mt0) REVERT: E 312 SER cc_start: 0.8008 (m) cc_final: 0.7620 (p) outliers start: 62 outliers final: 47 residues processed: 316 average time/residue: 1.1515 time to fit residues: 401.3819 Evaluate side-chains 338 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 282 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 282 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14425 Z= 0.218 Angle : 0.664 11.625 19590 Z= 0.329 Chirality : 0.044 0.141 2255 Planarity : 0.004 0.041 2420 Dihedral : 4.743 25.383 2190 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.16 % Allowed : 22.44 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1705 helix: 1.20 (0.24), residues: 550 sheet: -1.37 (0.25), residues: 390 loop : -1.14 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 422 HIS 0.001 0.000 HIS B 217 PHE 0.015 0.001 PHE C 322 TYR 0.013 0.001 TYR E 317 ARG 0.007 0.000 ARG E 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 284 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7259 (t80) REVERT: A 243 MET cc_start: 0.8228 (tpp) cc_final: 0.7597 (mtt) REVERT: A 312 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7524 (p) REVERT: A 391 MET cc_start: 0.5022 (pmm) cc_final: 0.4409 (pmm) REVERT: D 75 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7433 (ttm-80) REVERT: D 94 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7360 (t80) REVERT: D 126 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6711 (pm20) REVERT: D 206 LYS cc_start: 0.8246 (mttp) cc_final: 0.8007 (mttp) REVERT: D 210 ASP cc_start: 0.8004 (m-30) cc_final: 0.7599 (m-30) REVERT: D 227 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: D 262 MET cc_start: 0.7024 (mpp) cc_final: 0.6707 (tmt) REVERT: B 126 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7082 (pm20) REVERT: B 179 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7808 (mmt) REVERT: B 206 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8026 (mttm) REVERT: B 219 ASN cc_start: 0.8145 (p0) cc_final: 0.7807 (p0) REVERT: B 235 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: C 32 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8103 (tmtt) REVERT: C 94 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7111 (t80) REVERT: C 126 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6886 (pm20) REVERT: C 229 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7859 (mtp-110) REVERT: C 235 GLN cc_start: 0.8098 (mm110) cc_final: 0.7874 (mt0) REVERT: C 243 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7774 (mtt) REVERT: C 279 MET cc_start: 0.8699 (tpp) cc_final: 0.7115 (mpp) REVERT: C 312 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7639 (p) REVERT: E 75 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7524 (ttm-80) REVERT: E 94 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7391 (t80) REVERT: E 120 LYS cc_start: 0.8315 (tttp) cc_final: 0.8062 (tttt) REVERT: E 126 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6876 (pm20) REVERT: E 132 LYS cc_start: 0.7958 (mttm) cc_final: 0.7726 (mtmp) REVERT: E 138 LYS cc_start: 0.8903 (ttpp) cc_final: 0.8651 (tttt) REVERT: E 206 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7791 (mttm) REVERT: E 210 ASP cc_start: 0.8066 (m-30) cc_final: 0.7624 (m-30) REVERT: E 235 GLN cc_start: 0.8008 (mm110) cc_final: 0.7656 (mt0) REVERT: E 312 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7609 (p) REVERT: E 391 MET cc_start: 0.4674 (pmm) cc_final: 0.4154 (pmm) outliers start: 63 outliers final: 51 residues processed: 313 average time/residue: 1.1617 time to fit residues: 401.6233 Evaluate side-chains 341 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 279 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN D 282 GLN B 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116479 restraints weight = 16311.028| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.86 r_work: 0.3099 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14425 Z= 0.177 Angle : 0.645 10.564 19590 Z= 0.318 Chirality : 0.043 0.142 2255 Planarity : 0.004 0.042 2420 Dihedral : 4.533 21.717 2190 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.63 % Allowed : 23.30 % Favored : 73.07 % 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: -0.60 (0.21), residues: 1705 helix: 1.31 (0.24), residues: 550 sheet: -1.26 (0.25), residues: 390 loop : -1.15 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 186 HIS 0.001 0.000 HIS B 217 PHE 0.015 0.001 PHE C 322 TYR 0.012 0.001 TYR E 317 ARG 0.007 0.000 ARG E 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6765.22 seconds wall clock time: 121 minutes 38.25 seconds (7298.25 seconds total)