Starting phenix.real_space_refine on Sun Nov 17 02:32:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/11_2024/8fwt_29518.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/11_2024/8fwt_29518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/11_2024/8fwt_29518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/11_2024/8fwt_29518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/11_2024/8fwt_29518.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/11_2024/8fwt_29518.cif" } resolution = 3.09 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= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8016 2.51 5 N 2100 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12606 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.93, per 1000 atoms: 0.71 Number of scatterers: 12606 At special positions: 0 Unit cell: (143.59, 113.71, 84.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2422 8.00 N 2100 7.00 C 8016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG A1002 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 275 " " NAG C1002 " - " ASN C 412 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 67 " " NAG G 1 " - " ASN B 378 " " NAG H 1 " - " ASN B 67 " " NAG I 1 " - " ASN C 378 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN D 378 " " NAG L 1 " - " ASN D 67 " Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.5 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 39.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.970A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.988A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.518A pdb=" N ILE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.666A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.989A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.867A pdb=" N ARG A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.542A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.838A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.970A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.988A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.519A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.667A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.989A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.867A pdb=" N ARG B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.542A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.838A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.970A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.988A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.518A pdb=" N ILE C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.665A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.988A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.866A pdb=" N ARG C 270 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.542A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.838A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.970A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.987A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 removed outlier: 3.518A pdb=" N ILE D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.667A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.989A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.866A pdb=" N ARG D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 301 removed outlier: 3.543A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.838A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 7.070A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 203 removed outlier: 7.071A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 203 removed outlier: 7.070A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.071A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 199 through 203 removed outlier: 7.070A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AC2, first strand: chain 'D' and resid 392 through 394 412 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3904 1.34 - 1.46: 2145 1.46 - 1.57: 6711 1.57 - 1.69: 6 1.69 - 1.81: 120 Bond restraints: 12886 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.594 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.592 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " ideal model delta sigma weight residual 1.528 1.595 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 12881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 16237 1.83 - 3.65: 1017 3.65 - 5.48: 128 5.48 - 7.31: 51 7.31 - 9.13: 17 Bond angle restraints: 17450 Sorted by residual: angle pdb=" C ASN B 84 " pdb=" N LEU B 85 " pdb=" CA LEU B 85 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C ASN A 84 " pdb=" N LEU A 85 " pdb=" CA LEU A 85 " ideal model delta sigma weight residual 121.54 130.02 -8.48 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASN C 84 " pdb=" N LEU C 85 " pdb=" CA LEU C 85 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASN D 84 " pdb=" N LEU D 85 " pdb=" CA LEU D 85 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" N GLN B 302 " pdb=" CA GLN B 302 " pdb=" C GLN B 302 " ideal model delta sigma weight residual 111.17 116.31 -5.14 1.41e+00 5.03e-01 1.33e+01 ... (remaining 17445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.43: 7704 22.43 - 44.86: 231 44.86 - 67.29: 69 67.29 - 89.72: 56 89.72 - 112.15: 38 Dihedral angle restraints: 8098 sinusoidal: 3630 harmonic: 4468 Sorted by residual: dihedral pdb=" CA ARG A 300 " pdb=" C ARG A 300 " pdb=" N LEU A 301 " pdb=" CA LEU A 301 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG B 300 " pdb=" C ARG B 300 " pdb=" N LEU B 301 " pdb=" CA LEU B 301 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG C 300 " pdb=" C ARG C 300 " pdb=" N LEU C 301 " pdb=" CA LEU C 301 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 8095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 2016 0.224 - 0.448: 16 0.448 - 0.672: 0 0.672 - 0.897: 0 0.897 - 1.121: 2 Chirality restraints: 2034 Sorted by residual: chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 412 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 412 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 275 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 2031 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 412 " 0.026 2.00e-02 2.50e+03 2.66e-02 8.82e+00 pdb=" CG ASN D 412 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN D 412 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN D 412 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG D1002 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 67 " 0.026 2.00e-02 2.50e+03 2.64e-02 8.69e+00 pdb=" CG ASN C 67 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 67 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 67 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 108 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 109 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 109 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 109 " -0.038 5.00e-02 4.00e+02 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4060 2.85 - 3.36: 10940 3.36 - 3.87: 20395 3.87 - 4.39: 23873 4.39 - 4.90: 41969 Nonbonded interactions: 101237 Sorted by model distance: nonbonded pdb=" OE1 GLN D 119 " pdb=" NZ LYS D 135 " model vdw 2.333 3.120 nonbonded pdb=" OE1 GLN B 119 " pdb=" NZ LYS B 135 " model vdw 2.333 3.120 nonbonded pdb=" OE1 GLN C 119 " pdb=" NZ LYS C 135 " model vdw 2.333 3.120 nonbonded pdb=" OE1 GLN A 119 " pdb=" NZ LYS A 135 " model vdw 2.333 3.120 nonbonded pdb=" NH1 ARG A 374 " pdb=" OD2 ASP A 386 " model vdw 2.345 3.120 ... (remaining 101232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.830 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: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.320 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 12886 Z= 0.452 Angle : 1.043 9.131 17450 Z= 0.589 Chirality : 0.066 1.121 2034 Planarity : 0.007 0.069 2180 Dihedral : 16.224 112.152 5198 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.82 % Allowed : 3.06 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.15), residues: 1524 helix: -4.46 (0.08), residues: 584 sheet: -2.71 (0.28), residues: 304 loop : -3.46 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 134 HIS 0.011 0.002 HIS C 253 PHE 0.022 0.003 PHE C 107 TYR 0.016 0.002 TYR A 146 ARG 0.011 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 306 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7607 (ttmt) REVERT: A 351 LYS cc_start: 0.7780 (ttmp) cc_final: 0.7259 (pttm) REVERT: B 82 LYS cc_start: 0.8721 (mttp) cc_final: 0.8239 (mttp) REVERT: B 112 SER cc_start: 0.8483 (m) cc_final: 0.8050 (t) REVERT: B 133 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7577 (mmm160) REVERT: B 360 MET cc_start: 0.8250 (tpt) cc_final: 0.8039 (tpt) REVERT: B 390 ASP cc_start: 0.7685 (m-30) cc_final: 0.7483 (m-30) REVERT: B 400 GLU cc_start: 0.6822 (tt0) cc_final: 0.6356 (mm-30) REVERT: C 200 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7606 (ttmt) REVERT: C 323 MET cc_start: 0.8870 (tpp) cc_final: 0.8666 (tpp) REVERT: C 325 ASP cc_start: 0.8078 (m-30) cc_final: 0.7859 (m-30) REVERT: C 351 LYS cc_start: 0.7751 (ttmp) cc_final: 0.7241 (pttm) REVERT: D 82 LYS cc_start: 0.8706 (mttp) cc_final: 0.8223 (mttp) REVERT: D 112 SER cc_start: 0.8471 (m) cc_final: 0.8030 (t) REVERT: D 223 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7738 (mt-10) REVERT: D 360 MET cc_start: 0.8253 (tpt) cc_final: 0.8020 (tpt) REVERT: D 400 GLU cc_start: 0.6867 (tt0) cc_final: 0.6367 (mm-30) outliers start: 11 outliers final: 0 residues processed: 317 average time/residue: 0.3412 time to fit residues: 142.1769 Evaluate side-chains 190 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 367 HIS ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 141 ASN B 367 HIS C 34 HIS C 367 HIS ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 98 GLN D 131 GLN D 141 ASN D 367 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12886 Z= 0.245 Angle : 0.721 9.475 17450 Z= 0.351 Chirality : 0.051 0.472 2034 Planarity : 0.006 0.055 2180 Dihedral : 15.416 91.755 2274 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.04 % Allowed : 7.46 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.18), residues: 1524 helix: -2.42 (0.15), residues: 612 sheet: -2.27 (0.28), residues: 316 loop : -2.96 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 296 HIS 0.005 0.001 HIS B 253 PHE 0.021 0.002 PHE B 315 TYR 0.019 0.002 TYR D 195 ARG 0.006 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8077 (m-30) cc_final: 0.7842 (m-30) REVERT: A 335 GLN cc_start: 0.6566 (tt0) cc_final: 0.6357 (tm-30) REVERT: A 351 LYS cc_start: 0.7826 (ttmp) cc_final: 0.7592 (tptt) REVERT: B 37 ARG cc_start: 0.7678 (ttp-110) cc_final: 0.7442 (ttm170) REVERT: B 82 LYS cc_start: 0.8679 (mttp) cc_final: 0.8240 (mttp) REVERT: B 133 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7675 (mmm160) REVERT: B 198 ARG cc_start: 0.7277 (ttp-170) cc_final: 0.7072 (ttp-170) REVERT: B 288 GLN cc_start: 0.5414 (mp10) cc_final: 0.5071 (mp10) REVERT: B 329 VAL cc_start: 0.7856 (t) cc_final: 0.7554 (m) REVERT: B 360 MET cc_start: 0.8175 (tpt) cc_final: 0.7899 (tpt) REVERT: B 390 ASP cc_start: 0.7734 (m-30) cc_final: 0.7517 (m-30) REVERT: B 400 GLU cc_start: 0.6878 (tt0) cc_final: 0.6403 (mm-30) REVERT: C 325 ASP cc_start: 0.8044 (m-30) cc_final: 0.7810 (m-30) REVERT: C 351 LYS cc_start: 0.7826 (ttmp) cc_final: 0.7584 (tptt) REVERT: D 82 LYS cc_start: 0.8693 (mttp) cc_final: 0.8218 (mttp) REVERT: D 329 VAL cc_start: 0.7905 (t) cc_final: 0.7554 (m) REVERT: D 360 MET cc_start: 0.8195 (tpt) cc_final: 0.7904 (tpt) REVERT: D 400 GLU cc_start: 0.6866 (tt0) cc_final: 0.6350 (mm-30) outliers start: 14 outliers final: 7 residues processed: 213 average time/residue: 0.3064 time to fit residues: 88.9374 Evaluate side-chains 181 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 137 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 339 GLN B 34 HIS C 165 GLN D 34 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12886 Z= 0.206 Angle : 0.667 10.097 17450 Z= 0.319 Chirality : 0.048 0.393 2034 Planarity : 0.005 0.054 2180 Dihedral : 12.436 83.738 2274 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.64 % Allowed : 9.18 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.20), residues: 1524 helix: -0.81 (0.19), residues: 608 sheet: -2.03 (0.28), residues: 328 loop : -2.52 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 353 HIS 0.004 0.001 HIS B 253 PHE 0.019 0.001 PHE B 315 TYR 0.015 0.001 TYR A 252 ARG 0.004 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8023 (m-30) cc_final: 0.7766 (m-30) REVERT: B 82 LYS cc_start: 0.8698 (mttp) cc_final: 0.8247 (mttp) REVERT: B 97 ASP cc_start: 0.7034 (m-30) cc_final: 0.6766 (m-30) REVERT: B 133 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.7731 (mmm160) REVERT: B 160 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7951 (mt) REVERT: B 329 VAL cc_start: 0.7826 (t) cc_final: 0.7409 (m) REVERT: B 360 MET cc_start: 0.8131 (tpt) cc_final: 0.7839 (tpt) REVERT: B 361 SER cc_start: 0.7876 (m) cc_final: 0.7493 (p) REVERT: B 400 GLU cc_start: 0.6883 (tt0) cc_final: 0.6416 (mm-30) REVERT: C 325 ASP cc_start: 0.8015 (m-30) cc_final: 0.7761 (m-30) REVERT: C 351 LYS cc_start: 0.7800 (ttmp) cc_final: 0.7581 (tptt) REVERT: D 82 LYS cc_start: 0.8701 (mttp) cc_final: 0.8229 (mttp) REVERT: D 160 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7928 (mt) REVERT: D 248 MET cc_start: 0.8535 (mmm) cc_final: 0.7842 (mmm) REVERT: D 329 VAL cc_start: 0.7884 (t) cc_final: 0.7444 (m) REVERT: D 360 MET cc_start: 0.8126 (tpt) cc_final: 0.7803 (tpt) REVERT: D 361 SER cc_start: 0.7838 (m) cc_final: 0.7434 (p) REVERT: D 400 GLU cc_start: 0.6897 (tt0) cc_final: 0.6415 (mm-30) outliers start: 22 outliers final: 15 residues processed: 209 average time/residue: 0.2782 time to fit residues: 80.5990 Evaluate side-chains 195 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 146 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN B 336 GLN D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12886 Z= 0.168 Angle : 0.629 10.715 17450 Z= 0.299 Chirality : 0.047 0.372 2034 Planarity : 0.004 0.056 2180 Dihedral : 10.534 76.392 2274 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.09 % Allowed : 9.78 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.21), residues: 1524 helix: 0.02 (0.21), residues: 608 sheet: -1.76 (0.29), residues: 320 loop : -2.35 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS C 253 PHE 0.018 0.001 PHE D 315 TYR 0.022 0.001 TYR A 44 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7371 (mmm) cc_final: 0.7075 (mmm) REVERT: A 325 ASP cc_start: 0.7993 (m-30) cc_final: 0.7791 (m-30) REVERT: B 82 LYS cc_start: 0.8697 (mttp) cc_final: 0.8338 (mttp) REVERT: B 160 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7908 (mt) REVERT: B 248 MET cc_start: 0.8284 (mmm) cc_final: 0.7898 (mmm) REVERT: B 329 VAL cc_start: 0.7655 (t) cc_final: 0.7250 (m) REVERT: B 360 MET cc_start: 0.8136 (tpt) cc_final: 0.7688 (tpt) REVERT: B 361 SER cc_start: 0.7825 (m) cc_final: 0.7459 (p) REVERT: B 400 GLU cc_start: 0.6922 (tt0) cc_final: 0.6448 (mm-30) REVERT: C 325 ASP cc_start: 0.7940 (m-30) cc_final: 0.7719 (m-30) REVERT: C 351 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7401 (pttm) REVERT: D 82 LYS cc_start: 0.8728 (mttp) cc_final: 0.8344 (mttp) REVERT: D 160 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7880 (mt) REVERT: D 329 VAL cc_start: 0.7664 (t) cc_final: 0.7241 (m) REVERT: D 360 MET cc_start: 0.8116 (tpt) cc_final: 0.7699 (tpt) REVERT: D 361 SER cc_start: 0.7840 (m) cc_final: 0.7461 (p) REVERT: D 400 GLU cc_start: 0.6948 (tt0) cc_final: 0.6476 (mm-30) outliers start: 28 outliers final: 15 residues processed: 199 average time/residue: 0.2891 time to fit residues: 80.3128 Evaluate side-chains 192 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 0.2980 chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12886 Z= 0.233 Angle : 0.636 10.820 17450 Z= 0.303 Chirality : 0.047 0.354 2034 Planarity : 0.004 0.056 2180 Dihedral : 9.404 65.850 2274 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.16 % Allowed : 11.04 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.22), residues: 1524 helix: 0.36 (0.21), residues: 612 sheet: -1.68 (0.30), residues: 328 loop : -2.24 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS D 253 PHE 0.016 0.002 PHE A 107 TYR 0.019 0.002 TYR A 44 ARG 0.003 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7487 (mmm) cc_final: 0.7268 (mmm) REVERT: A 325 ASP cc_start: 0.8007 (m-30) cc_final: 0.7801 (m-30) REVERT: B 82 LYS cc_start: 0.8742 (mttp) cc_final: 0.8338 (mttp) REVERT: B 97 ASP cc_start: 0.7019 (m-30) cc_final: 0.6791 (m-30) REVERT: B 160 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7999 (mt) REVERT: B 194 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5838 (ptt90) REVERT: B 329 VAL cc_start: 0.7690 (t) cc_final: 0.7292 (m) REVERT: B 360 MET cc_start: 0.8211 (tpt) cc_final: 0.7673 (tpt) REVERT: B 361 SER cc_start: 0.7846 (m) cc_final: 0.7468 (p) REVERT: B 400 GLU cc_start: 0.7037 (tt0) cc_final: 0.6570 (mm-30) REVERT: C 351 LYS cc_start: 0.7733 (ttmp) cc_final: 0.7394 (pttm) REVERT: D 82 LYS cc_start: 0.8751 (mttp) cc_final: 0.8344 (mttp) REVERT: D 160 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7962 (mt) REVERT: D 194 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.5809 (ptt90) REVERT: D 248 MET cc_start: 0.8466 (mmm) cc_final: 0.7929 (mmm) REVERT: D 329 VAL cc_start: 0.7683 (t) cc_final: 0.7237 (m) REVERT: D 361 SER cc_start: 0.7852 (m) cc_final: 0.7452 (p) REVERT: D 400 GLU cc_start: 0.7022 (tt0) cc_final: 0.6537 (mm-30) outliers start: 29 outliers final: 18 residues processed: 194 average time/residue: 0.3006 time to fit residues: 80.6883 Evaluate side-chains 181 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9980 chunk 132 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN B 336 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12886 Z= 0.250 Angle : 0.638 10.284 17450 Z= 0.305 Chirality : 0.047 0.355 2034 Planarity : 0.004 0.057 2180 Dihedral : 8.711 55.896 2274 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.16 % Allowed : 11.34 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.22), residues: 1524 helix: 0.46 (0.21), residues: 612 sheet: -1.68 (0.30), residues: 328 loop : -2.20 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 296 HIS 0.004 0.001 HIS D 232 PHE 0.016 0.001 PHE C 107 TYR 0.014 0.002 TYR A 146 ARG 0.003 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.492 Fit side-chains REVERT: A 247 MET cc_start: 0.7404 (mmm) cc_final: 0.7180 (mmm) REVERT: A 294 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 365 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7309 (pt0) REVERT: B 82 LYS cc_start: 0.8795 (mttp) cc_final: 0.8381 (mttp) REVERT: B 160 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 194 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5746 (ptt90) REVERT: B 329 VAL cc_start: 0.7798 (t) cc_final: 0.7339 (m) REVERT: B 340 MET cc_start: 0.7798 (ttm) cc_final: 0.7497 (ttp) REVERT: B 361 SER cc_start: 0.7820 (m) cc_final: 0.7428 (p) REVERT: B 400 GLU cc_start: 0.7032 (tt0) cc_final: 0.6576 (mm-30) REVERT: C 335 GLN cc_start: 0.6901 (tm-30) cc_final: 0.6694 (tm-30) REVERT: C 351 LYS cc_start: 0.7744 (ttmp) cc_final: 0.7414 (pttm) REVERT: D 82 LYS cc_start: 0.8790 (mttp) cc_final: 0.8374 (mttp) REVERT: D 160 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7962 (mt) REVERT: D 194 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.5671 (ptt90) REVERT: D 329 VAL cc_start: 0.7791 (t) cc_final: 0.7332 (m) REVERT: D 340 MET cc_start: 0.7831 (ttm) cc_final: 0.7524 (ttp) REVERT: D 361 SER cc_start: 0.7810 (m) cc_final: 0.7394 (p) REVERT: D 400 GLU cc_start: 0.7042 (tt0) cc_final: 0.6581 (mm-30) outliers start: 29 outliers final: 22 residues processed: 184 average time/residue: 0.3058 time to fit residues: 77.8429 Evaluate side-chains 178 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.0030 chunk 16 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12886 Z= 0.167 Angle : 0.596 9.444 17450 Z= 0.285 Chirality : 0.045 0.346 2034 Planarity : 0.004 0.055 2180 Dihedral : 7.982 55.775 2274 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.46 % Allowed : 12.09 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1524 helix: 0.67 (0.21), residues: 612 sheet: -1.50 (0.30), residues: 328 loop : -2.11 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS C 253 PHE 0.016 0.001 PHE B 315 TYR 0.015 0.001 TYR A 146 ARG 0.003 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7298 (mmm) cc_final: 0.7089 (mmm) REVERT: B 82 LYS cc_start: 0.8800 (mttp) cc_final: 0.8388 (mttp) REVERT: B 97 ASP cc_start: 0.6985 (m-30) cc_final: 0.6771 (m-30) REVERT: B 329 VAL cc_start: 0.7676 (t) cc_final: 0.7268 (m) REVERT: B 340 MET cc_start: 0.7843 (ttm) cc_final: 0.7493 (ttp) REVERT: B 361 SER cc_start: 0.7817 (m) cc_final: 0.7437 (p) REVERT: B 400 GLU cc_start: 0.7033 (tt0) cc_final: 0.6545 (mm-30) REVERT: C 351 LYS cc_start: 0.7764 (ttmp) cc_final: 0.7427 (pttm) REVERT: D 82 LYS cc_start: 0.8808 (mttp) cc_final: 0.8371 (mttp) REVERT: D 329 VAL cc_start: 0.7710 (t) cc_final: 0.7270 (m) REVERT: D 340 MET cc_start: 0.7855 (ttm) cc_final: 0.7514 (ttp) REVERT: D 360 MET cc_start: 0.8157 (tpt) cc_final: 0.7713 (tpt) REVERT: D 361 SER cc_start: 0.7783 (m) cc_final: 0.7396 (p) REVERT: D 400 GLU cc_start: 0.7053 (tt0) cc_final: 0.6557 (mm-30) outliers start: 33 outliers final: 22 residues processed: 197 average time/residue: 0.3208 time to fit residues: 87.7086 Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12886 Z= 0.245 Angle : 0.625 8.693 17450 Z= 0.300 Chirality : 0.046 0.341 2034 Planarity : 0.004 0.056 2180 Dihedral : 7.693 56.273 2274 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.16 % Allowed : 12.54 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1524 helix: 0.64 (0.21), residues: 612 sheet: -1.66 (0.30), residues: 332 loop : -2.04 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 169 HIS 0.004 0.001 HIS D 232 PHE 0.016 0.001 PHE B 315 TYR 0.018 0.002 TYR A 44 ARG 0.004 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7221 (mmm) cc_final: 0.6981 (mmm) REVERT: A 294 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 82 LYS cc_start: 0.8778 (mttp) cc_final: 0.8337 (mttp) REVERT: B 97 ASP cc_start: 0.7004 (m-30) cc_final: 0.6795 (m-30) REVERT: B 340 MET cc_start: 0.7853 (ttm) cc_final: 0.7536 (ttp) REVERT: B 361 SER cc_start: 0.7841 (m) cc_final: 0.7443 (p) REVERT: B 400 GLU cc_start: 0.7082 (tt0) cc_final: 0.6601 (mm-30) REVERT: C 294 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7318 (mm-30) REVERT: C 351 LYS cc_start: 0.7763 (ttmp) cc_final: 0.7546 (pttm) REVERT: D 82 LYS cc_start: 0.8805 (mttp) cc_final: 0.8360 (mttp) REVERT: D 340 MET cc_start: 0.7893 (ttm) cc_final: 0.7576 (ttp) REVERT: D 360 MET cc_start: 0.8184 (tpt) cc_final: 0.7676 (tpt) REVERT: D 361 SER cc_start: 0.7792 (m) cc_final: 0.7450 (p) REVERT: D 400 GLU cc_start: 0.7057 (tt0) cc_final: 0.6600 (mm-30) outliers start: 29 outliers final: 25 residues processed: 187 average time/residue: 0.2903 time to fit residues: 75.6700 Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12886 Z= 0.225 Angle : 0.615 8.228 17450 Z= 0.297 Chirality : 0.046 0.333 2034 Planarity : 0.004 0.056 2180 Dihedral : 7.406 56.011 2274 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.16 % Allowed : 13.13 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1524 helix: 0.70 (0.21), residues: 612 sheet: -1.53 (0.31), residues: 328 loop : -1.99 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 169 HIS 0.004 0.001 HIS A 34 PHE 0.016 0.001 PHE B 315 TYR 0.016 0.001 TYR B 86 ARG 0.004 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7264 (mmm) cc_final: 0.7045 (mmm) REVERT: A 294 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7370 (mm-30) REVERT: B 82 LYS cc_start: 0.8789 (mttp) cc_final: 0.8322 (mttp) REVERT: B 340 MET cc_start: 0.7889 (ttm) cc_final: 0.7627 (ttp) REVERT: B 361 SER cc_start: 0.7841 (m) cc_final: 0.7452 (p) REVERT: B 400 GLU cc_start: 0.7087 (tt0) cc_final: 0.6613 (mm-30) REVERT: C 294 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7324 (mm-30) REVERT: C 351 LYS cc_start: 0.7809 (ttmp) cc_final: 0.7464 (pttm) REVERT: D 82 LYS cc_start: 0.8816 (mttp) cc_final: 0.8365 (mttp) REVERT: D 340 MET cc_start: 0.7954 (ttm) cc_final: 0.7663 (ttp) REVERT: D 361 SER cc_start: 0.7812 (m) cc_final: 0.7364 (p) REVERT: D 400 GLU cc_start: 0.7059 (tt0) cc_final: 0.6604 (mm-30) outliers start: 29 outliers final: 28 residues processed: 180 average time/residue: 0.3026 time to fit residues: 75.2554 Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 151 optimal weight: 0.1980 chunk 139 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 95 optimal weight: 0.0370 chunk 128 optimal weight: 0.8980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12886 Z= 0.171 Angle : 0.589 7.744 17450 Z= 0.285 Chirality : 0.045 0.329 2034 Planarity : 0.004 0.056 2180 Dihedral : 7.159 55.837 2274 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.72 % Allowed : 13.58 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1524 helix: 0.90 (0.22), residues: 612 sheet: -1.42 (0.30), residues: 332 loop : -1.92 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS A 34 PHE 0.017 0.001 PHE B 315 TYR 0.016 0.001 TYR A 146 ARG 0.004 0.000 ARG A 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 82 LYS cc_start: 0.8783 (mttp) cc_final: 0.8322 (mttp) REVERT: B 340 MET cc_start: 0.7937 (ttm) cc_final: 0.7709 (ttp) REVERT: B 361 SER cc_start: 0.7868 (m) cc_final: 0.7481 (p) REVERT: B 400 GLU cc_start: 0.7052 (tt0) cc_final: 0.6578 (mm-30) REVERT: C 294 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7311 (mm-30) REVERT: C 351 LYS cc_start: 0.7769 (ttmp) cc_final: 0.7472 (pttm) REVERT: D 82 LYS cc_start: 0.8808 (mttp) cc_final: 0.8334 (mttp) REVERT: D 340 MET cc_start: 0.7971 (ttm) cc_final: 0.7733 (ttp) REVERT: D 361 SER cc_start: 0.7734 (m) cc_final: 0.7349 (p) REVERT: D 400 GLU cc_start: 0.7013 (tt0) cc_final: 0.6570 (mm-30) outliers start: 23 outliers final: 22 residues processed: 177 average time/residue: 0.3034 time to fit residues: 74.9216 Evaluate side-chains 180 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.177628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.140155 restraints weight = 13013.810| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.31 r_work: 0.3157 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12886 Z= 0.214 Angle : 0.600 7.866 17450 Z= 0.290 Chirality : 0.045 0.328 2034 Planarity : 0.004 0.055 2180 Dihedral : 7.096 56.136 2274 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.94 % Allowed : 13.51 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1524 helix: 0.91 (0.21), residues: 612 sheet: -1.49 (0.30), residues: 328 loop : -1.81 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 169 HIS 0.004 0.001 HIS A 34 PHE 0.018 0.001 PHE B 315 TYR 0.016 0.001 TYR A 146 ARG 0.004 0.000 ARG A 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3050.80 seconds wall clock time: 56 minutes 35.22 seconds (3395.22 seconds total)