Starting phenix.real_space_refine on Sat Jan 20 10:56:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/01_2024/5ljv_4062_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/01_2024/5ljv_4062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/01_2024/5ljv_4062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/01_2024/5ljv_4062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/01_2024/5ljv_4062_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ljv_4062/01_2024/5ljv_4062_updated.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 72 5.16 5 C 9474 2.51 5 N 2580 2.21 5 O 2856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15000 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "B" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "C" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "E" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "F" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.38, per 1000 atoms: 0.56 Number of scatterers: 15000 At special positions: 0 Unit cell: (97.82, 92.46, 187.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 12 15.00 Mg 6 11.99 O 2856 8.00 N 2580 7.00 C 9474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 3.0 seconds 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 24 sheets defined 42.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.541A pdb=" N LYS A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 66 removed outlier: 5.450A pdb=" N SER A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 189 through 201 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.551A pdb=" N ALA A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 258 through 271 removed outlier: 3.644A pdb=" N SER A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 4.718A pdb=" N ALA A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 Processing helix chain 'A' and resid 296 through 307 Proline residue: A 306 - end of helix Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.528A pdb=" N LYS B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 66 removed outlier: 5.444A pdb=" N SER B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 101 removed outlier: 3.906A pdb=" N GLU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.584A pdb=" N ALA B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 271 removed outlier: 3.616A pdb=" N SER B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 removed outlier: 4.707A pdb=" N ALA B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 Processing helix chain 'B' and resid 296 through 307 Proline residue: B 306 - end of helix Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'C' and resid 45 through 51 removed outlier: 3.530A pdb=" N LYS C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 66 removed outlier: 5.437A pdb=" N SER C 66 " --> pdb=" O PHE C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 101 Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.884A pdb=" N ARG C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.563A pdb=" N ALA C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 258 through 271 removed outlier: 3.624A pdb=" N SER C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 removed outlier: 4.715A pdb=" N ALA C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N THR C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 292 Processing helix chain 'C' and resid 296 through 307 Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'D' and resid 45 through 51 removed outlier: 3.537A pdb=" N LYS D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 66 removed outlier: 5.439A pdb=" N SER D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 101 Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'D' and resid 189 through 203 removed outlier: 3.891A pdb=" N ARG D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.575A pdb=" N ALA D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 258 through 271 removed outlier: 3.633A pdb=" N SER D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 removed outlier: 4.716A pdb=" N ALA D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 292 Processing helix chain 'D' and resid 296 through 307 Proline residue: D 306 - end of helix Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'E' and resid 45 through 51 removed outlier: 3.537A pdb=" N LYS E 49 " --> pdb=" O VAL E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 66 removed outlier: 5.438A pdb=" N SER E 66 " --> pdb=" O PHE E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 101 removed outlier: 3.912A pdb=" N GLU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'E' and resid 143 through 151 Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'E' and resid 211 through 221 removed outlier: 3.595A pdb=" N ALA E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 Processing helix chain 'E' and resid 258 through 271 removed outlier: 3.630A pdb=" N SER E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 283 removed outlier: 4.709A pdb=" N ALA E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN E 283 " --> pdb=" O THR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 292 Processing helix chain 'E' and resid 296 through 307 Proline residue: E 306 - end of helix Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.549A pdb=" N LYS F 49 " --> pdb=" O VAL F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 66 removed outlier: 5.443A pdb=" N SER F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 101 Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'F' and resid 143 through 151 Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 211 through 221 removed outlier: 3.569A pdb=" N ALA F 216 " --> pdb=" O ASN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 Processing helix chain 'F' and resid 258 through 271 removed outlier: 3.648A pdb=" N SER F 271 " --> pdb=" O THR F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 283 removed outlier: 5.039A pdb=" N ALA F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 292 Processing helix chain 'F' and resid 296 through 307 Proline residue: F 306 - end of helix Processing helix chain 'F' and resid 321 through 330 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 36 removed outlier: 5.677A pdb=" N GLU A 108 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A 14 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N CYS A 110 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL A 16 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL A 112 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 137 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE A 113 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU A 139 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 115 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 141 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 39 through 42 Processing sheet with id= C, first strand: chain 'A' and resid 285 through 287 Processing sheet with id= D, first strand: chain 'A' and resid 232 through 237 Processing sheet with id= E, first strand: chain 'B' and resid 32 through 36 removed outlier: 5.701A pdb=" N GLU B 108 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU B 14 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS B 110 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 16 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL B 112 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR B 137 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 113 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 139 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 115 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 141 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 39 through 42 Processing sheet with id= G, first strand: chain 'B' and resid 285 through 287 removed outlier: 3.922A pdb=" N THR B 157 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 232 through 237 Processing sheet with id= I, first strand: chain 'C' and resid 32 through 36 removed outlier: 5.718A pdb=" N GLU C 108 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU C 14 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS C 110 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL C 16 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL C 112 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU C 18 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY C 114 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C 137 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE C 113 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU C 139 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 115 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL C 141 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 39 through 42 Processing sheet with id= K, first strand: chain 'C' and resid 285 through 287 Processing sheet with id= L, first strand: chain 'C' and resid 232 through 237 Processing sheet with id= M, first strand: chain 'D' and resid 32 through 36 removed outlier: 5.707A pdb=" N GLU D 108 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU D 14 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS D 110 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL D 16 " --> pdb=" O CYS D 110 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL D 112 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 18 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY D 114 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR D 137 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE D 113 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU D 139 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL D 115 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 141 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 39 through 42 Processing sheet with id= O, first strand: chain 'D' and resid 285 through 287 Processing sheet with id= P, first strand: chain 'D' and resid 232 through 237 Processing sheet with id= Q, first strand: chain 'E' and resid 32 through 36 removed outlier: 5.694A pdb=" N GLU E 108 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU E 14 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N CYS E 110 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL E 16 " --> pdb=" O CYS E 110 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E 112 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 18 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY E 114 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR E 137 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE E 113 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU E 139 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL E 115 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL E 141 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 39 through 42 Processing sheet with id= S, first strand: chain 'E' and resid 285 through 287 Processing sheet with id= T, first strand: chain 'E' and resid 232 through 237 Processing sheet with id= U, first strand: chain 'F' and resid 32 through 36 removed outlier: 5.666A pdb=" N GLU F 108 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU F 14 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS F 110 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL F 16 " --> pdb=" O CYS F 110 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL F 112 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR F 137 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE F 113 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU F 139 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 115 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL F 141 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 39 through 42 Processing sheet with id= W, first strand: chain 'F' and resid 285 through 287 Processing sheet with id= X, first strand: chain 'F' and resid 232 through 237 650 hydrogen bonds defined for protein. 1842 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: 5.10 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 2365 1.26 - 1.42: 3797 1.42 - 1.57: 8777 1.57 - 1.72: 211 1.72 - 1.87: 108 Bond restraints: 15258 Sorted by residual: bond pdb=" CA HIS A 22 " pdb=" C HIS A 22 " ideal model delta sigma weight residual 1.520 1.374 0.146 1.21e-02 6.83e+03 1.46e+02 bond pdb=" CA VAL C 160 " pdb=" C VAL C 160 " ideal model delta sigma weight residual 1.527 1.426 0.101 8.50e-03 1.38e+04 1.41e+02 bond pdb=" CA HIS F 22 " pdb=" C HIS F 22 " ideal model delta sigma weight residual 1.520 1.377 0.144 1.21e-02 6.83e+03 1.41e+02 bond pdb=" CA VAL D 160 " pdb=" C VAL D 160 " ideal model delta sigma weight residual 1.527 1.429 0.097 8.50e-03 1.38e+04 1.31e+02 bond pdb=" CA VAL D 183 " pdb=" CB VAL D 183 " ideal model delta sigma weight residual 1.550 1.435 0.115 1.03e-02 9.43e+03 1.25e+02 ... (remaining 15253 not shown) Histogram of bond angle deviations from ideal: 91.91 - 100.40: 133 100.40 - 108.90: 3029 108.90 - 117.39: 8684 117.39 - 125.89: 8661 125.89 - 134.38: 229 Bond angle restraints: 20736 Sorted by residual: angle pdb=" C VAL E 147 " pdb=" CA VAL E 147 " pdb=" CB VAL E 147 " ideal model delta sigma weight residual 111.97 98.86 13.11 1.28e+00 6.10e-01 1.05e+02 angle pdb=" C VAL B 147 " pdb=" CA VAL B 147 " pdb=" CB VAL B 147 " ideal model delta sigma weight residual 111.97 99.07 12.90 1.28e+00 6.10e-01 1.01e+02 angle pdb=" C VAL D 147 " pdb=" CA VAL D 147 " pdb=" CB VAL D 147 " ideal model delta sigma weight residual 111.97 99.35 12.62 1.28e+00 6.10e-01 9.73e+01 angle pdb=" C VAL C 147 " pdb=" CA VAL C 147 " pdb=" CB VAL C 147 " ideal model delta sigma weight residual 111.81 99.72 12.09 1.25e+00 6.40e-01 9.35e+01 angle pdb=" C VAL F 147 " pdb=" CA VAL F 147 " pdb=" CB VAL F 147 " ideal model delta sigma weight residual 111.97 100.08 11.89 1.28e+00 6.10e-01 8.63e+01 ... (remaining 20731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.13: 7969 20.13 - 40.27: 1016 40.27 - 60.40: 269 60.40 - 80.53: 20 80.53 - 100.67: 14 Dihedral angle restraints: 9288 sinusoidal: 3708 harmonic: 5580 Sorted by residual: dihedral pdb=" C MET D 258 " pdb=" N MET D 258 " pdb=" CA MET D 258 " pdb=" CB MET D 258 " ideal model delta harmonic sigma weight residual -122.60 -142.76 20.16 0 2.50e+00 1.60e-01 6.50e+01 dihedral pdb=" C MET C 258 " pdb=" N MET C 258 " pdb=" CA MET C 258 " pdb=" CB MET C 258 " ideal model delta harmonic sigma weight residual -122.60 -142.34 19.74 0 2.50e+00 1.60e-01 6.23e+01 dihedral pdb=" C MET E 258 " pdb=" N MET E 258 " pdb=" CA MET E 258 " pdb=" CB MET E 258 " ideal model delta harmonic sigma weight residual -122.60 -142.24 19.64 0 2.50e+00 1.60e-01 6.17e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 2035 0.192 - 0.384: 340 0.384 - 0.576: 49 0.576 - 0.768: 6 0.768 - 0.960: 6 Chirality restraints: 2436 Sorted by residual: chirality pdb=" CA MET F 258 " pdb=" N MET F 258 " pdb=" C MET F 258 " pdb=" CB MET F 258 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" CA MET E 258 " pdb=" N MET E 258 " pdb=" C MET E 258 " pdb=" CB MET E 258 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CA MET A 258 " pdb=" N MET A 258 " pdb=" C MET A 258 " pdb=" CB MET A 258 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.25e+01 ... (remaining 2433 not shown) Planarity restraints: 2676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 67 " 0.069 2.00e-02 2.50e+03 4.21e-02 3.55e+01 pdb=" CG TYR F 67 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR F 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 67 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR F 67 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR F 67 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR F 67 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR F 67 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 286 " -0.063 2.00e-02 2.50e+03 4.45e-02 3.47e+01 pdb=" CG PHE E 286 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 PHE E 286 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 286 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE E 286 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 286 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE E 286 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " 0.064 2.00e-02 2.50e+03 3.90e-02 3.04e+01 pdb=" CG TYR A 67 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " -0.005 2.00e-02 2.50e+03 ... (remaining 2673 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 833 2.64 - 3.20: 15441 3.20 - 3.77: 25332 3.77 - 4.33: 35597 4.33 - 4.90: 55144 Nonbonded interactions: 132347 Sorted by model distance: nonbonded pdb=" NZ LYS A 49 " pdb=" OH TYR C 149 " model vdw 2.070 2.520 nonbonded pdb=" OH TYR D 149 " pdb=" NZ LYS F 49 " model vdw 2.075 2.520 nonbonded pdb=" OH TYR A 149 " pdb=" NZ LYS B 49 " model vdw 2.106 2.520 nonbonded pdb=" NZ LYS E 49 " pdb=" OH TYR F 149 " model vdw 2.132 2.520 nonbonded pdb=" O THR D 20 " pdb=" OG1 THR D 20 " model vdw 2.181 2.440 ... (remaining 132342 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' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.620 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 44.440 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.030 0.189 15258 Z= 1.992 Angle : 2.849 21.364 20736 Z= 1.714 Chirality : 0.155 0.960 2436 Planarity : 0.016 0.126 2676 Dihedral : 18.809 100.668 5700 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 2.89 % Allowed : 7.38 % Favored : 89.73 % Rotamer: Outliers : 11.82 % Allowed : 13.25 % Favored : 74.94 % Cbeta Deviations : 4.74 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.82 % 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: -4.53 (0.15), residues: 1938 helix: -3.57 (0.11), residues: 870 sheet: -0.64 (0.27), residues: 306 loop : -3.16 (0.18), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.006 HIS E 22 PHE 0.093 0.013 PHE E 286 TYR 0.083 0.015 TYR F 67 ARG 0.010 0.002 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 507 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7884 (p90) REVERT: A 63 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: A 84 ASP cc_start: 0.8938 (m-30) cc_final: 0.8416 (t0) REVERT: A 100 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.9003 (t) REVERT: A 112 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.8843 (p) REVERT: A 126 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8191 (tp) REVERT: A 136 HIS cc_start: 0.8070 (p90) cc_final: 0.7799 (p90) REVERT: A 166 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9026 (p) REVERT: A 180 GLU cc_start: 0.8894 (mp0) cc_final: 0.8650 (tp30) REVERT: A 185 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7962 (mm) REVERT: A 209 MET cc_start: 0.8559 (mtm) cc_final: 0.8089 (mtm) REVERT: A 249 PRO cc_start: 0.8970 (Cg_exo) cc_final: 0.8729 (Cg_endo) REVERT: A 302 GLU cc_start: 0.8662 (tp30) cc_final: 0.8434 (tp30) REVERT: A 331 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8968 (tp30) REVERT: B 84 ASP cc_start: 0.8701 (m-30) cc_final: 0.8372 (t0) REVERT: B 109 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7385 (mm) REVERT: B 180 GLU cc_start: 0.9280 (mp0) cc_final: 0.9045 (tp30) REVERT: B 194 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7901 (tt0) REVERT: B 202 GLU cc_start: 0.8659 (tt0) cc_final: 0.8359 (mt-10) REVERT: B 209 MET cc_start: 0.8639 (mtm) cc_final: 0.8005 (mtm) REVERT: B 259 PRO cc_start: 0.8362 (OUTLIER) cc_final: 0.8093 (Cg_exo) REVERT: B 270 ARG cc_start: 0.8521 (ptt180) cc_final: 0.7943 (mmt180) REVERT: B 317 ASP cc_start: 0.7993 (t0) cc_final: 0.7184 (p0) REVERT: C 26 MET cc_start: 0.8722 (mtp) cc_final: 0.8486 (mtm) REVERT: C 51 LEU cc_start: 0.9260 (tp) cc_final: 0.8637 (tp) REVERT: C 59 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8283 (t70) REVERT: C 64 MET cc_start: 0.7739 (mtt) cc_final: 0.7507 (mtt) REVERT: C 75 GLN cc_start: 0.8702 (pm20) cc_final: 0.8448 (pt0) REVERT: C 109 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7877 (mp) REVERT: C 112 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.8822 (p) REVERT: C 126 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 146 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8476 (ptt) REVERT: C 154 LEU cc_start: 0.8347 (mt) cc_final: 0.7992 (mt) REVERT: C 180 GLU cc_start: 0.9122 (mp0) cc_final: 0.8758 (tp30) REVERT: C 240 LYS cc_start: 0.7704 (mttt) cc_final: 0.7420 (tptt) REVERT: C 249 PRO cc_start: 0.9129 (Cg_exo) cc_final: 0.8880 (Cg_endo) REVERT: C 275 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8769 (tm-30) REVERT: D 26 MET cc_start: 0.8569 (mtp) cc_final: 0.8325 (mtm) REVERT: D 32 LYS cc_start: 0.8682 (mttt) cc_final: 0.8290 (mtpp) REVERT: D 51 LEU cc_start: 0.9279 (tp) cc_final: 0.8662 (tp) REVERT: D 59 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8245 (t70) REVERT: D 72 TYR cc_start: 0.8898 (m-80) cc_final: 0.8669 (m-80) REVERT: D 74 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8849 (mt) REVERT: D 109 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7978 (mp) REVERT: D 112 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9047 (m) REVERT: D 126 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8468 (tt) REVERT: D 146 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8374 (ptt) REVERT: D 149 TYR cc_start: 0.9047 (t80) cc_final: 0.8768 (t80) REVERT: D 154 LEU cc_start: 0.8270 (mt) cc_final: 0.7941 (mt) REVERT: D 180 GLU cc_start: 0.9127 (mp0) cc_final: 0.8724 (tp30) REVERT: D 194 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8051 (tt0) REVERT: D 198 ASN cc_start: 0.8982 (m-40) cc_final: 0.8748 (m110) REVERT: D 220 GLN cc_start: 0.8791 (tt0) cc_final: 0.8474 (tt0) REVERT: D 240 LYS cc_start: 0.7724 (mttt) cc_final: 0.7436 (tptt) REVERT: D 275 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8836 (tm-30) REVERT: E 69 ASP cc_start: 0.8908 (t0) cc_final: 0.8514 (p0) REVERT: E 109 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7299 (mm) REVERT: E 112 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9061 (t) REVERT: E 167 THR cc_start: 0.9237 (m) cc_final: 0.8794 (p) REVERT: E 180 GLU cc_start: 0.9271 (mp0) cc_final: 0.9014 (tm-30) REVERT: E 187 LYS cc_start: 0.8689 (mttt) cc_final: 0.8392 (mtmt) REVERT: E 195 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8050 (tpt-90) REVERT: E 204 HIS cc_start: 0.8279 (m90) cc_final: 0.8045 (m90) REVERT: E 209 MET cc_start: 0.8676 (mtm) cc_final: 0.8292 (mtm) REVERT: E 229 GLU cc_start: 0.8556 (pt0) cc_final: 0.8254 (pm20) REVERT: E 252 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8447 (mm) REVERT: E 259 PRO cc_start: 0.8492 (OUTLIER) cc_final: 0.8256 (Cg_exo) REVERT: E 270 ARG cc_start: 0.8504 (ptt180) cc_final: 0.7892 (mtt180) REVERT: E 302 GLU cc_start: 0.8927 (tp30) cc_final: 0.8688 (tp30) REVERT: E 317 ASP cc_start: 0.7863 (t0) cc_final: 0.6951 (p0) REVERT: F 13 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8057 (p90) REVERT: F 20 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8785 (t) REVERT: F 51 LEU cc_start: 0.8861 (tp) cc_final: 0.8648 (tp) REVERT: F 55 TYR cc_start: 0.8923 (p90) cc_final: 0.8472 (p90) REVERT: F 81 GLU cc_start: 0.8403 (tt0) cc_final: 0.8004 (tp30) REVERT: F 84 ASP cc_start: 0.8998 (m-30) cc_final: 0.8583 (t0) REVERT: F 100 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.8996 (t) REVERT: F 112 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.8818 (m) REVERT: F 136 HIS cc_start: 0.8038 (p90) cc_final: 0.7735 (p90) REVERT: F 137 THR cc_start: 0.9074 (m) cc_final: 0.8766 (p) REVERT: F 143 GLU cc_start: 0.8742 (tt0) cc_final: 0.8020 (tp30) REVERT: F 166 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9116 (p) REVERT: F 168 ASP cc_start: 0.8731 (m-30) cc_final: 0.8488 (m-30) REVERT: F 180 GLU cc_start: 0.8911 (mp0) cc_final: 0.8640 (tp30) REVERT: F 185 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8233 (mm) REVERT: F 209 MET cc_start: 0.8543 (mtm) cc_final: 0.8075 (mtm) REVERT: F 249 PRO cc_start: 0.8988 (Cg_exo) cc_final: 0.8783 (Cg_endo) outliers start: 190 outliers final: 37 residues processed: 627 average time/residue: 0.2716 time to fit residues: 245.8908 Evaluate side-chains 352 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 284 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 259 PRO Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 259 PRO Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 PRO Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 259 PRO Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 195 ARG Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 259 PRO Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 259 PRO Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 267 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 136 HIS A 198 ASN B 92 HIS B 132 GLN B 198 ASN C 92 HIS C 198 ASN C 212 ASN D 92 HIS D 132 GLN D 182 GLN D 198 ASN D 212 ASN E 92 HIS E 132 GLN E 136 HIS E 198 ASN E 212 ASN F 92 HIS F 198 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15258 Z= 0.298 Angle : 0.861 8.284 20736 Z= 0.420 Chirality : 0.050 0.179 2436 Planarity : 0.007 0.069 2676 Dihedral : 11.510 101.167 2284 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 6.97 % Allowed : 19.03 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.22 (0.17), residues: 1938 helix: -1.42 (0.15), residues: 918 sheet: -0.61 (0.24), residues: 324 loop : -1.72 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 136 PHE 0.014 0.002 PHE D 13 TYR 0.016 0.002 TYR A 191 ARG 0.006 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 374 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8743 (t) REVERT: A 84 ASP cc_start: 0.8817 (m-30) cc_final: 0.8586 (t0) REVERT: A 100 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8635 (t) REVERT: A 108 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: A 112 VAL cc_start: 0.9320 (t) cc_final: 0.9051 (m) REVERT: A 136 HIS cc_start: 0.8082 (p-80) cc_final: 0.7674 (p-80) REVERT: A 181 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8538 (p0) REVERT: A 194 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7577 (mp0) REVERT: A 208 GLN cc_start: 0.8261 (mt0) cc_final: 0.7950 (mt0) REVERT: A 212 ASN cc_start: 0.8542 (m-40) cc_final: 0.7802 (t0) REVERT: A 276 TYR cc_start: 0.8477 (m-80) cc_final: 0.8147 (m-80) REVERT: B 69 ASP cc_start: 0.8685 (t0) cc_final: 0.8215 (p0) REVERT: B 112 VAL cc_start: 0.9297 (t) cc_final: 0.8968 (m) REVERT: B 132 GLN cc_start: 0.8298 (mt0) cc_final: 0.8074 (mt0) REVERT: B 181 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8403 (p0) REVERT: B 182 GLN cc_start: 0.8993 (mt0) cc_final: 0.8781 (mt0) REVERT: B 209 MET cc_start: 0.8435 (mtm) cc_final: 0.8222 (mtp) REVERT: B 211 VAL cc_start: 0.8715 (m) cc_final: 0.8366 (t) REVERT: B 220 GLN cc_start: 0.9058 (tt0) cc_final: 0.8778 (mm-40) REVERT: B 270 ARG cc_start: 0.8333 (ptt180) cc_final: 0.7469 (mmt180) REVERT: C 13 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: C 14 LEU cc_start: 0.9050 (mt) cc_final: 0.8817 (mt) REVERT: C 26 MET cc_start: 0.8727 (mtp) cc_final: 0.8402 (mtm) REVERT: C 32 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8076 (mtpp) REVERT: C 74 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8614 (mt) REVERT: C 75 GLN cc_start: 0.8371 (pm20) cc_final: 0.8158 (pt0) REVERT: C 109 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8024 (mp) REVERT: C 112 VAL cc_start: 0.9259 (t) cc_final: 0.9056 (p) REVERT: C 123 ASN cc_start: 0.8909 (m110) cc_final: 0.8638 (m110) REVERT: C 181 ASP cc_start: 0.8611 (m-30) cc_final: 0.8387 (p0) REVERT: C 182 GLN cc_start: 0.8357 (mt0) cc_final: 0.8142 (mt0) REVERT: C 211 VAL cc_start: 0.8827 (m) cc_final: 0.8443 (t) REVERT: C 220 GLN cc_start: 0.8840 (tt0) cc_final: 0.8547 (mt0) REVERT: C 240 LYS cc_start: 0.7969 (mttt) cc_final: 0.7582 (tptt) REVERT: C 252 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7959 (mm) REVERT: C 275 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8646 (mp0) REVERT: D 14 LEU cc_start: 0.9063 (mt) cc_final: 0.8830 (mt) REVERT: D 20 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9197 (t) REVERT: D 32 LYS cc_start: 0.8398 (mttt) cc_final: 0.8092 (ttpt) REVERT: D 59 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7830 (t70) REVERT: D 72 TYR cc_start: 0.8852 (m-80) cc_final: 0.8557 (m-80) REVERT: D 123 ASN cc_start: 0.8949 (m110) cc_final: 0.8646 (m110) REVERT: D 211 VAL cc_start: 0.8864 (m) cc_final: 0.8423 (t) REVERT: D 220 GLN cc_start: 0.8808 (tt0) cc_final: 0.8526 (mt0) REVERT: D 240 LYS cc_start: 0.8004 (mttt) cc_final: 0.7650 (tptt) REVERT: D 275 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8629 (mp0) REVERT: D 311 ASN cc_start: 0.8127 (t0) cc_final: 0.7899 (t0) REVERT: E 69 ASP cc_start: 0.8908 (t0) cc_final: 0.8594 (p0) REVERT: E 130 MET cc_start: 0.8648 (tpp) cc_final: 0.8409 (mmt) REVERT: E 132 GLN cc_start: 0.8271 (mt0) cc_final: 0.8056 (mt0) REVERT: E 181 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8600 (p0) REVERT: E 182 GLN cc_start: 0.8881 (mt0) cc_final: 0.8661 (mt0) REVERT: E 202 GLU cc_start: 0.8669 (tt0) cc_final: 0.8451 (mt-10) REVERT: E 211 VAL cc_start: 0.8736 (m) cc_final: 0.8511 (p) REVERT: E 220 GLN cc_start: 0.8974 (tt0) cc_final: 0.8645 (mm-40) REVERT: E 270 ARG cc_start: 0.8313 (ptt180) cc_final: 0.7498 (mmt180) REVERT: F 20 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8769 (t) REVERT: F 84 ASP cc_start: 0.8855 (m-30) cc_final: 0.8628 (t0) REVERT: F 100 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8652 (t) REVERT: F 108 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7433 (mm-30) REVERT: F 112 VAL cc_start: 0.9316 (t) cc_final: 0.9101 (m) REVERT: F 130 MET cc_start: 0.8530 (tpp) cc_final: 0.8187 (mmp) REVERT: F 132 GLN cc_start: 0.8188 (mt0) cc_final: 0.7932 (mt0) REVERT: F 136 HIS cc_start: 0.8310 (p90) cc_final: 0.7864 (p90) REVERT: F 194 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7728 (mp0) REVERT: F 208 GLN cc_start: 0.8216 (mt0) cc_final: 0.7975 (mt0) REVERT: F 212 ASN cc_start: 0.8539 (m-40) cc_final: 0.7735 (t0) REVERT: F 276 TYR cc_start: 0.8442 (m-80) cc_final: 0.8207 (m-80) outliers start: 112 outliers final: 44 residues processed: 453 average time/residue: 0.2451 time to fit residues: 170.4131 Evaluate side-chains 351 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 291 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 140 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 123 ASN B 182 GLN B 198 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN D 182 GLN E 10 ASN E 182 GLN E 198 ASN E 212 ASN E 282 GLN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15258 Z= 0.250 Angle : 0.749 7.792 20736 Z= 0.358 Chirality : 0.047 0.161 2436 Planarity : 0.006 0.054 2676 Dihedral : 9.043 95.152 2194 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.29 % Allowed : 22.89 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.09 (0.18), residues: 1938 helix: -0.56 (0.16), residues: 924 sheet: 0.01 (0.26), residues: 288 loop : -1.04 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 136 PHE 0.011 0.001 PHE D 235 TYR 0.012 0.001 TYR A 191 ARG 0.005 0.001 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 352 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: A 20 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8755 (t) REVERT: A 50 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8670 (tt) REVERT: A 136 HIS cc_start: 0.8059 (p-80) cc_final: 0.7602 (p-80) REVERT: A 194 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7662 (mp0) REVERT: A 276 TYR cc_start: 0.8353 (m-80) cc_final: 0.8072 (m-80) REVERT: B 69 ASP cc_start: 0.8774 (t0) cc_final: 0.8353 (p0) REVERT: B 112 VAL cc_start: 0.9303 (t) cc_final: 0.9045 (m) REVERT: B 132 GLN cc_start: 0.8277 (mt0) cc_final: 0.7995 (mt0) REVERT: B 220 GLN cc_start: 0.9008 (tt0) cc_final: 0.8747 (mm-40) REVERT: B 270 ARG cc_start: 0.8330 (ptt180) cc_final: 0.7480 (mmt180) REVERT: C 26 MET cc_start: 0.8883 (mtp) cc_final: 0.8512 (mtm) REVERT: C 74 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8504 (mt) REVERT: C 109 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8070 (mp) REVERT: C 149 TYR cc_start: 0.8561 (t80) cc_final: 0.8292 (t80) REVERT: C 181 ASP cc_start: 0.8671 (m-30) cc_final: 0.8375 (p0) REVERT: C 208 GLN cc_start: 0.8253 (mt0) cc_final: 0.7239 (pp30) REVERT: C 211 VAL cc_start: 0.8722 (m) cc_final: 0.8495 (t) REVERT: C 220 GLN cc_start: 0.8839 (tt0) cc_final: 0.8559 (mt0) REVERT: C 240 LYS cc_start: 0.8018 (mttt) cc_final: 0.7631 (tptt) REVERT: C 275 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8970 (mp0) REVERT: D 75 GLN cc_start: 0.8581 (mp10) cc_final: 0.7957 (pt0) REVERT: D 109 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8082 (mp) REVERT: D 211 VAL cc_start: 0.8804 (m) cc_final: 0.8478 (t) REVERT: D 220 GLN cc_start: 0.8828 (tt0) cc_final: 0.8559 (mt0) REVERT: D 240 LYS cc_start: 0.8174 (mttt) cc_final: 0.7829 (tptt) REVERT: D 275 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8684 (mp0) REVERT: E 69 ASP cc_start: 0.8999 (t0) cc_final: 0.8619 (p0) REVERT: E 76 ASP cc_start: 0.8777 (m-30) cc_final: 0.8333 (t70) REVERT: E 132 GLN cc_start: 0.8348 (mt0) cc_final: 0.8061 (mt0) REVERT: E 202 GLU cc_start: 0.8429 (tt0) cc_final: 0.8223 (mt-10) REVERT: E 211 VAL cc_start: 0.8603 (m) cc_final: 0.8321 (t) REVERT: E 220 GLN cc_start: 0.8956 (tt0) cc_final: 0.8685 (mm-40) REVERT: E 270 ARG cc_start: 0.8211 (ptt180) cc_final: 0.7404 (mmm160) REVERT: E 317 ASP cc_start: 0.6999 (t0) cc_final: 0.6429 (t70) REVERT: F 132 GLN cc_start: 0.8188 (mt0) cc_final: 0.7895 (mt0) REVERT: F 136 HIS cc_start: 0.8362 (p90) cc_final: 0.7674 (p-80) REVERT: F 194 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7657 (mp0) REVERT: F 208 GLN cc_start: 0.8087 (mt0) cc_final: 0.7886 (mt0) REVERT: F 212 ASN cc_start: 0.8386 (m-40) cc_final: 0.7579 (t0) outliers start: 69 outliers final: 39 residues processed: 396 average time/residue: 0.2156 time to fit residues: 134.8494 Evaluate side-chains 336 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 291 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 166 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN B 182 GLN C 182 GLN E 123 ASN E 156 ASN E 182 GLN F 136 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15258 Z= 0.223 Angle : 0.697 7.809 20736 Z= 0.331 Chirality : 0.046 0.155 2436 Planarity : 0.005 0.052 2676 Dihedral : 7.967 86.371 2182 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.29 % Allowed : 23.57 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.49 (0.18), residues: 1938 helix: -0.06 (0.16), residues: 918 sheet: 0.38 (0.25), residues: 312 loop : -0.82 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 136 PHE 0.014 0.001 PHE F 307 TYR 0.009 0.001 TYR E 41 ARG 0.003 0.000 ARG F 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 309 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8689 (t) REVERT: A 26 MET cc_start: 0.8605 (mtm) cc_final: 0.8393 (mtm) REVERT: A 136 HIS cc_start: 0.8105 (p-80) cc_final: 0.7648 (p-80) REVERT: A 194 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7832 (mp0) REVERT: A 276 TYR cc_start: 0.8267 (m-80) cc_final: 0.7976 (m-80) REVERT: A 302 GLU cc_start: 0.8253 (tp30) cc_final: 0.8031 (tp30) REVERT: B 76 ASP cc_start: 0.8947 (m-30) cc_final: 0.8522 (t70) REVERT: B 112 VAL cc_start: 0.9267 (t) cc_final: 0.8973 (m) REVERT: B 220 GLN cc_start: 0.8971 (tt0) cc_final: 0.8727 (mm-40) REVERT: B 258 MET cc_start: 0.8639 (mmt) cc_final: 0.8261 (mmt) REVERT: B 261 ILE cc_start: 0.8948 (mt) cc_final: 0.8671 (tt) REVERT: B 270 ARG cc_start: 0.8169 (ptt180) cc_final: 0.7377 (mmt-90) REVERT: C 26 MET cc_start: 0.8863 (mtp) cc_final: 0.8554 (mtm) REVERT: C 74 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8471 (mt) REVERT: C 82 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8225 (tt) REVERT: C 109 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7787 (mp) REVERT: C 149 TYR cc_start: 0.8582 (t80) cc_final: 0.8319 (t80) REVERT: C 181 ASP cc_start: 0.8711 (m-30) cc_final: 0.8394 (p0) REVERT: C 208 GLN cc_start: 0.8169 (mt0) cc_final: 0.7256 (pp30) REVERT: C 211 VAL cc_start: 0.8670 (m) cc_final: 0.8468 (t) REVERT: C 220 GLN cc_start: 0.8844 (tt0) cc_final: 0.8558 (mt0) REVERT: C 240 LYS cc_start: 0.8192 (mttt) cc_final: 0.7809 (mmtt) REVERT: C 275 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8959 (mp0) REVERT: C 302 GLU cc_start: 0.8472 (tp30) cc_final: 0.8230 (mm-30) REVERT: D 75 GLN cc_start: 0.8330 (mp10) cc_final: 0.7864 (pt0) REVERT: D 109 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8091 (mp) REVERT: D 149 TYR cc_start: 0.8470 (t80) cc_final: 0.8186 (t80) REVERT: D 208 GLN cc_start: 0.8305 (mt0) cc_final: 0.7388 (pp30) REVERT: D 220 GLN cc_start: 0.8838 (tt0) cc_final: 0.8554 (mt0) REVERT: D 275 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8998 (mp0) REVERT: D 302 GLU cc_start: 0.8492 (tp30) cc_final: 0.8267 (mm-30) REVERT: E 44 ASP cc_start: 0.8884 (p0) cc_final: 0.8679 (p0) REVERT: E 69 ASP cc_start: 0.8992 (t0) cc_final: 0.8616 (p0) REVERT: E 202 GLU cc_start: 0.8427 (tt0) cc_final: 0.8173 (mt-10) REVERT: E 220 GLN cc_start: 0.8933 (tt0) cc_final: 0.8669 (mm-40) REVERT: E 270 ARG cc_start: 0.8187 (ptt180) cc_final: 0.7373 (mmt-90) REVERT: F 136 HIS cc_start: 0.8072 (p-80) cc_final: 0.7730 (p-80) REVERT: F 194 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7655 (mp0) REVERT: F 208 GLN cc_start: 0.8139 (mt0) cc_final: 0.7925 (mt0) outliers start: 69 outliers final: 42 residues processed: 360 average time/residue: 0.2228 time to fit residues: 124.4502 Evaluate side-chains 328 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 281 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 265 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.0970 chunk 105 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 158 optimal weight: 0.0270 chunk 128 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 182 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 182 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 182 GLN F 123 ASN F 182 GLN F 282 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15258 Z= 0.196 Angle : 0.660 6.860 20736 Z= 0.311 Chirality : 0.045 0.139 2436 Planarity : 0.005 0.050 2676 Dihedral : 7.505 80.029 2178 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.54 % Allowed : 24.56 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.17 (0.18), residues: 1938 helix: 0.21 (0.17), residues: 918 sheet: 0.63 (0.26), residues: 330 loop : -0.75 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 136 PHE 0.009 0.001 PHE A 13 TYR 0.010 0.001 TYR E 41 ARG 0.004 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 308 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: A 20 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8683 (t) REVERT: A 136 HIS cc_start: 0.8152 (p-80) cc_final: 0.7719 (p-80) REVERT: A 194 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7805 (mp0) REVERT: A 276 TYR cc_start: 0.8269 (m-80) cc_final: 0.7976 (m-80) REVERT: A 302 GLU cc_start: 0.8257 (tp30) cc_final: 0.8045 (tp30) REVERT: B 41 TYR cc_start: 0.8503 (m-10) cc_final: 0.8135 (m-10) REVERT: B 69 ASP cc_start: 0.8793 (t0) cc_final: 0.8550 (p0) REVERT: B 76 ASP cc_start: 0.8960 (m-30) cc_final: 0.8553 (t70) REVERT: B 132 GLN cc_start: 0.8046 (mt0) cc_final: 0.7740 (mm-40) REVERT: B 209 MET cc_start: 0.8106 (mtp) cc_final: 0.7870 (mtp) REVERT: B 220 GLN cc_start: 0.8947 (tt0) cc_final: 0.8699 (mm-40) REVERT: B 270 ARG cc_start: 0.8157 (ptt180) cc_final: 0.7402 (mmt90) REVERT: C 26 MET cc_start: 0.8863 (mtp) cc_final: 0.8563 (mtm) REVERT: C 132 GLN cc_start: 0.8360 (mt0) cc_final: 0.7937 (mm-40) REVERT: C 149 TYR cc_start: 0.8463 (t80) cc_final: 0.8186 (t80) REVERT: C 181 ASP cc_start: 0.8701 (m-30) cc_final: 0.8397 (p0) REVERT: C 208 GLN cc_start: 0.8099 (mt0) cc_final: 0.7270 (pp30) REVERT: C 220 GLN cc_start: 0.8838 (tt0) cc_final: 0.8553 (mt0) REVERT: C 240 LYS cc_start: 0.8274 (mttt) cc_final: 0.7851 (mmtt) REVERT: C 275 GLU cc_start: 0.9217 (mt-10) cc_final: 0.9008 (mp0) REVERT: C 302 GLU cc_start: 0.8492 (tp30) cc_final: 0.8233 (mm-30) REVERT: D 109 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8018 (mp) REVERT: D 208 GLN cc_start: 0.8271 (mt0) cc_final: 0.7434 (pp30) REVERT: D 220 GLN cc_start: 0.8831 (tt0) cc_final: 0.8546 (mt0) REVERT: D 275 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8996 (mp0) REVERT: D 302 GLU cc_start: 0.8501 (tp30) cc_final: 0.8261 (mm-30) REVERT: E 69 ASP cc_start: 0.9005 (t0) cc_final: 0.8622 (p0) REVERT: E 76 ASP cc_start: 0.8967 (m-30) cc_final: 0.8583 (t70) REVERT: E 202 GLU cc_start: 0.8385 (tt0) cc_final: 0.8123 (mt-10) REVERT: E 220 GLN cc_start: 0.8918 (tt0) cc_final: 0.8645 (mm-40) REVERT: E 258 MET cc_start: 0.8410 (mmt) cc_final: 0.8090 (mmt) REVERT: E 270 ARG cc_start: 0.8121 (ptt180) cc_final: 0.7375 (mmt-90) REVERT: E 317 ASP cc_start: 0.6729 (t0) cc_final: 0.6520 (t70) REVERT: F 44 ASP cc_start: 0.9211 (p0) cc_final: 0.8972 (p0) REVERT: F 136 HIS cc_start: 0.8002 (p-80) cc_final: 0.7703 (p-80) REVERT: F 194 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7632 (mp0) outliers start: 57 outliers final: 42 residues processed: 348 average time/residue: 0.2266 time to fit residues: 121.6829 Evaluate side-chains 313 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 269 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN B 10 ASN B 182 GLN B 208 GLN C 182 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN E 10 ASN E 182 GLN E 208 GLN F 277 GLN F 282 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15258 Z= 0.447 Angle : 0.775 7.082 20736 Z= 0.371 Chirality : 0.050 0.197 2436 Planarity : 0.005 0.053 2676 Dihedral : 7.495 80.763 2176 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.60 % Allowed : 23.69 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.61 (0.18), residues: 1938 helix: -0.17 (0.16), residues: 912 sheet: 0.30 (0.25), residues: 330 loop : -0.90 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 136 PHE 0.020 0.002 PHE C 233 TYR 0.016 0.001 TYR C 67 ARG 0.005 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 275 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.9014 (mtp) cc_final: 0.8450 (mtm) REVERT: A 136 HIS cc_start: 0.8054 (p-80) cc_final: 0.7674 (p-80) REVERT: A 194 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7661 (mp0) REVERT: A 276 TYR cc_start: 0.8352 (m-80) cc_final: 0.8013 (m-80) REVERT: B 75 GLN cc_start: 0.8271 (pm20) cc_final: 0.7885 (tp40) REVERT: B 76 ASP cc_start: 0.9058 (m-30) cc_final: 0.8643 (t70) REVERT: B 220 GLN cc_start: 0.8965 (tt0) cc_final: 0.8706 (mm-40) REVERT: B 270 ARG cc_start: 0.8372 (ptt180) cc_final: 0.7568 (mmt-90) REVERT: C 26 MET cc_start: 0.8899 (mtp) cc_final: 0.8644 (mtm) REVERT: C 82 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8088 (tt) REVERT: C 109 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7920 (mp) REVERT: C 132 GLN cc_start: 0.8420 (mt0) cc_final: 0.8034 (mm-40) REVERT: C 149 TYR cc_start: 0.8697 (t80) cc_final: 0.8467 (t80) REVERT: C 181 ASP cc_start: 0.8770 (m-30) cc_final: 0.8486 (p0) REVERT: C 208 GLN cc_start: 0.8144 (mt0) cc_final: 0.7160 (pp30) REVERT: C 220 GLN cc_start: 0.8765 (tt0) cc_final: 0.8500 (mt0) REVERT: C 240 LYS cc_start: 0.8413 (mttt) cc_final: 0.8029 (mmtt) REVERT: C 275 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8928 (mp0) REVERT: C 302 GLU cc_start: 0.8595 (tp30) cc_final: 0.8314 (mm-30) REVERT: D 109 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8046 (mp) REVERT: D 132 GLN cc_start: 0.8422 (mt0) cc_final: 0.8053 (mm-40) REVERT: D 220 GLN cc_start: 0.8772 (tt0) cc_final: 0.8507 (mt0) REVERT: D 275 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8930 (mp0) REVERT: E 69 ASP cc_start: 0.8954 (t0) cc_final: 0.8517 (p0) REVERT: E 75 GLN cc_start: 0.8280 (pm20) cc_final: 0.7894 (tp-100) REVERT: E 202 GLU cc_start: 0.8575 (tt0) cc_final: 0.8317 (mt-10) REVERT: E 270 ARG cc_start: 0.8399 (ptt180) cc_final: 0.7554 (mmt-90) REVERT: F 136 HIS cc_start: 0.8006 (p-80) cc_final: 0.7702 (p-80) REVERT: F 194 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7690 (mp0) REVERT: F 208 GLN cc_start: 0.8337 (mt0) cc_final: 0.7920 (mt0) outliers start: 74 outliers final: 51 residues processed: 328 average time/residue: 0.2273 time to fit residues: 115.6993 Evaluate side-chains 308 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 254 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 276 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.0010 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 182 GLN C 182 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 136 HIS E 182 GLN E 212 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15258 Z= 0.220 Angle : 0.678 7.284 20736 Z= 0.321 Chirality : 0.045 0.168 2436 Planarity : 0.005 0.051 2676 Dihedral : 7.136 76.855 2175 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.54 % Allowed : 25.81 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.28 (0.18), residues: 1938 helix: 0.11 (0.17), residues: 918 sheet: 0.28 (0.26), residues: 342 loop : -0.63 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 136 PHE 0.017 0.001 PHE A 223 TYR 0.010 0.001 TYR E 41 ARG 0.005 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 292 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8935 (mtp) cc_final: 0.8332 (mtm) REVERT: A 136 HIS cc_start: 0.8064 (p-80) cc_final: 0.7645 (p-80) REVERT: A 194 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7755 (mp0) REVERT: A 276 TYR cc_start: 0.8287 (m-80) cc_final: 0.7939 (m-80) REVERT: B 75 GLN cc_start: 0.8282 (pm20) cc_final: 0.7905 (tp40) REVERT: B 76 ASP cc_start: 0.8963 (m-30) cc_final: 0.8492 (t0) REVERT: B 132 GLN cc_start: 0.8066 (mt0) cc_final: 0.7789 (mm-40) REVERT: B 209 MET cc_start: 0.8004 (mtp) cc_final: 0.7763 (mtp) REVERT: B 220 GLN cc_start: 0.8897 (tt0) cc_final: 0.8651 (mm-40) REVERT: B 270 ARG cc_start: 0.8471 (ptt180) cc_final: 0.7651 (mmt-90) REVERT: C 26 MET cc_start: 0.8912 (mtp) cc_final: 0.8636 (mtm) REVERT: C 132 GLN cc_start: 0.8364 (mt0) cc_final: 0.7999 (mm-40) REVERT: C 149 TYR cc_start: 0.8666 (t80) cc_final: 0.8422 (t80) REVERT: C 181 ASP cc_start: 0.8761 (m-30) cc_final: 0.8499 (p0) REVERT: C 208 GLN cc_start: 0.8163 (mt0) cc_final: 0.7211 (pp30) REVERT: C 220 GLN cc_start: 0.8751 (tt0) cc_final: 0.8489 (mt0) REVERT: C 240 LYS cc_start: 0.8403 (mttt) cc_final: 0.8006 (mmpt) REVERT: C 275 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8991 (mp0) REVERT: C 302 GLU cc_start: 0.8538 (tp30) cc_final: 0.8264 (mm-30) REVERT: D 86 ASP cc_start: 0.8449 (m-30) cc_final: 0.8188 (m-30) REVERT: D 109 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7991 (mp) REVERT: D 132 GLN cc_start: 0.8373 (mt0) cc_final: 0.8063 (mm-40) REVERT: D 149 TYR cc_start: 0.8625 (t80) cc_final: 0.8411 (t80) REVERT: D 208 GLN cc_start: 0.8328 (mt0) cc_final: 0.7247 (pp30) REVERT: D 220 GLN cc_start: 0.8772 (tt0) cc_final: 0.8486 (mt0) REVERT: D 275 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8967 (mp0) REVERT: D 302 GLU cc_start: 0.8557 (tp30) cc_final: 0.8283 (mm-30) REVERT: E 41 TYR cc_start: 0.8520 (m-10) cc_final: 0.8014 (m-10) REVERT: E 69 ASP cc_start: 0.8980 (t0) cc_final: 0.8460 (p0) REVERT: E 75 GLN cc_start: 0.8297 (pm20) cc_final: 0.7963 (tp-100) REVERT: E 76 ASP cc_start: 0.8812 (m-30) cc_final: 0.8325 (t0) REVERT: E 132 GLN cc_start: 0.8065 (mt0) cc_final: 0.7613 (mm-40) REVERT: E 202 GLU cc_start: 0.8437 (tt0) cc_final: 0.8196 (mt-10) REVERT: E 270 ARG cc_start: 0.8342 (ptt180) cc_final: 0.7497 (mmt180) REVERT: E 317 ASP cc_start: 0.6902 (t0) cc_final: 0.6530 (t70) REVERT: F 136 HIS cc_start: 0.7992 (p-80) cc_final: 0.7690 (p-80) REVERT: F 194 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7624 (mp0) REVERT: F 208 GLN cc_start: 0.8295 (mt0) cc_final: 0.7925 (mt0) outliers start: 57 outliers final: 42 residues processed: 334 average time/residue: 0.2218 time to fit residues: 115.3744 Evaluate side-chains 315 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 272 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 276 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN B 182 GLN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN E 182 GLN E 208 GLN E 212 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15258 Z= 0.369 Angle : 0.727 7.625 20736 Z= 0.346 Chirality : 0.048 0.170 2436 Planarity : 0.005 0.081 2676 Dihedral : 7.224 77.223 2175 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.42 % Allowed : 25.87 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 1938 helix: -0.01 (0.17), residues: 918 sheet: 0.12 (0.26), residues: 342 loop : -0.63 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 136 PHE 0.014 0.002 PHE A 223 TYR 0.013 0.001 TYR E 41 ARG 0.004 0.000 ARG E 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 272 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8932 (mtp) cc_final: 0.8364 (mtm) REVERT: A 136 HIS cc_start: 0.7986 (p-80) cc_final: 0.7592 (p-80) REVERT: A 194 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7664 (mp0) REVERT: A 276 TYR cc_start: 0.8315 (m-80) cc_final: 0.7964 (m-80) REVERT: B 75 GLN cc_start: 0.8285 (pm20) cc_final: 0.7929 (tp40) REVERT: B 76 ASP cc_start: 0.9042 (m-30) cc_final: 0.8638 (t0) REVERT: B 132 GLN cc_start: 0.8097 (mt0) cc_final: 0.7824 (mm-40) REVERT: B 220 GLN cc_start: 0.8938 (tt0) cc_final: 0.8672 (mm-40) REVERT: B 270 ARG cc_start: 0.8397 (ptt180) cc_final: 0.7489 (mmt-90) REVERT: C 26 MET cc_start: 0.8916 (mtp) cc_final: 0.8659 (mtm) REVERT: C 109 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7903 (mp) REVERT: C 132 GLN cc_start: 0.8382 (mt0) cc_final: 0.8030 (mm-40) REVERT: C 149 TYR cc_start: 0.8659 (t80) cc_final: 0.8434 (t80) REVERT: C 181 ASP cc_start: 0.8722 (m-30) cc_final: 0.8456 (p0) REVERT: C 208 GLN cc_start: 0.8139 (mt0) cc_final: 0.7236 (pp30) REVERT: C 220 GLN cc_start: 0.8743 (tt0) cc_final: 0.8486 (mt0) REVERT: C 240 LYS cc_start: 0.8420 (mttt) cc_final: 0.8035 (mmpt) REVERT: C 275 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8907 (mp0) REVERT: C 302 GLU cc_start: 0.8561 (tp30) cc_final: 0.8282 (mm-30) REVERT: D 109 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8060 (mp) REVERT: D 132 GLN cc_start: 0.8400 (mt0) cc_final: 0.8096 (mm-40) REVERT: D 149 TYR cc_start: 0.8627 (t80) cc_final: 0.8380 (t80) REVERT: D 220 GLN cc_start: 0.8726 (tt0) cc_final: 0.8454 (mt0) REVERT: D 224 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8560 (m) REVERT: D 275 GLU cc_start: 0.9249 (mt-10) cc_final: 0.9006 (mp0) REVERT: D 302 GLU cc_start: 0.8572 (tp30) cc_final: 0.8305 (mm-30) REVERT: E 69 ASP cc_start: 0.8818 (t0) cc_final: 0.8462 (p0) REVERT: E 75 GLN cc_start: 0.8312 (pm20) cc_final: 0.8007 (tp-100) REVERT: E 76 ASP cc_start: 0.8851 (m-30) cc_final: 0.8411 (t0) REVERT: E 132 GLN cc_start: 0.8081 (mt0) cc_final: 0.7798 (mm-40) REVERT: E 202 GLU cc_start: 0.8446 (tt0) cc_final: 0.8196 (mt-10) REVERT: E 270 ARG cc_start: 0.8417 (ptt180) cc_final: 0.7591 (mmt-90) REVERT: F 41 TYR cc_start: 0.8730 (m-10) cc_final: 0.8432 (m-10) REVERT: F 136 HIS cc_start: 0.7874 (p-80) cc_final: 0.7660 (p-80) REVERT: F 194 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7701 (mp0) outliers start: 71 outliers final: 54 residues processed: 326 average time/residue: 0.2228 time to fit residues: 113.1793 Evaluate side-chains 326 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 269 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 276 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.4598 > 50: distance: 29 - 34: 10.755 distance: 34 - 35: 7.588 distance: 34 - 185: 14.022 distance: 35 - 36: 8.947 distance: 35 - 38: 8.895 distance: 36 - 37: 15.725 distance: 36 - 41: 18.197 distance: 37 - 182: 22.191 distance: 38 - 39: 19.114 distance: 38 - 40: 11.969 distance: 41 - 42: 9.758 distance: 42 - 43: 8.880 distance: 43 - 44: 6.104 distance: 43 - 45: 8.502 distance: 45 - 46: 8.718 distance: 45 - 174: 9.138 distance: 46 - 47: 5.706 distance: 46 - 49: 3.538 distance: 47 - 48: 5.317 distance: 47 - 57: 6.770 distance: 48 - 171: 17.338 distance: 49 - 50: 7.951 distance: 50 - 51: 8.561 distance: 50 - 52: 20.992 distance: 51 - 53: 3.898 distance: 52 - 54: 3.899 distance: 53 - 55: 16.347 distance: 54 - 55: 12.802 distance: 55 - 56: 3.184 distance: 57 - 58: 16.212 distance: 57 - 63: 18.645 distance: 58 - 59: 12.106 distance: 58 - 61: 16.421 distance: 59 - 60: 10.488 distance: 59 - 64: 3.998 distance: 61 - 62: 21.849 distance: 62 - 63: 6.384 distance: 64 - 65: 11.272 distance: 65 - 66: 6.473 distance: 65 - 68: 5.301 distance: 66 - 67: 27.420 distance: 66 - 73: 12.812 distance: 68 - 69: 6.242 distance: 69 - 70: 9.034 distance: 70 - 71: 12.091 distance: 71 - 72: 9.949 distance: 73 - 74: 5.797 distance: 74 - 75: 11.504 distance: 74 - 77: 5.166 distance: 75 - 76: 9.695 distance: 75 - 81: 11.774 distance: 77 - 78: 7.160 distance: 78 - 80: 3.763 distance: 81 - 82: 15.381 distance: 82 - 83: 19.679 distance: 82 - 85: 19.865 distance: 83 - 84: 19.050 distance: 83 - 88: 37.762 distance: 85 - 86: 14.407 distance: 85 - 87: 12.128 distance: 88 - 89: 15.097 distance: 89 - 90: 10.361 distance: 89 - 92: 16.659 distance: 90 - 91: 16.392 distance: 90 - 96: 8.182 distance: 91 - 115: 25.486 distance: 92 - 93: 23.409 distance: 92 - 94: 4.404 distance: 93 - 95: 15.521 distance: 96 - 97: 22.516 distance: 97 - 98: 16.057 distance: 98 - 99: 11.692 distance: 98 - 100: 7.057 distance: 99 - 122: 23.418 distance: 100 - 101: 17.853 distance: 101 - 102: 6.328 distance: 101 - 104: 18.851 distance: 102 - 103: 11.533 distance: 102 - 108: 18.371 distance: 104 - 105: 10.650 distance: 105 - 106: 35.988 distance: 105 - 107: 33.541