Starting phenix.real_space_refine on Thu Feb 15 15:01:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/02_2024/8fwt_29518.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/02_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_29518/02_2024/8fwt_29518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/02_2024/8fwt_29518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/02_2024/8fwt_29518.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwt_29518/02_2024/8fwt_29518.pdb" } 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 Residue "A ARG 58": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.75, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 4.74 Conformation dependent library (CDL) restraints added in 2.2 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: 1.28 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: 3.21 Time building geometry restraints manager: 5.15 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: 98.74 - 105.78: 275 105.78 - 112.83: 6919 112.83 - 119.88: 4138 119.88 - 126.92: 5953 126.92 - 133.97: 165 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 2.520 nonbonded pdb=" OE1 GLN B 119 " pdb=" NZ LYS B 135 " model vdw 2.333 2.520 nonbonded pdb=" OE1 GLN C 119 " pdb=" NZ LYS C 135 " model vdw 2.333 2.520 nonbonded pdb=" OE1 GLN A 119 " pdb=" NZ LYS A 135 " model vdw 2.333 2.520 nonbonded pdb=" NH1 ARG A 374 " pdb=" OD2 ASP A 386 " model vdw 2.345 2.520 ... (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 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.610 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 33.520 Find NCS groups from input model: 0.780 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.860 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 11 poor density : 306 time to evaluate : 1.387 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: 0.3321 time to fit residues: 138.3523 Evaluate side-chains 190 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 367 HIS B 73 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 367 HIS C 367 HIS ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 367 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12886 Z= 0.271 Angle : 0.719 9.702 17450 Z= 0.351 Chirality : 0.050 0.471 2034 Planarity : 0.006 0.055 2180 Dihedral : 15.635 90.838 2274 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.12 % Allowed : 8.21 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.18), residues: 1524 helix: -2.51 (0.15), residues: 612 sheet: -2.32 (0.28), residues: 320 loop : -2.90 (0.22), residues: 592 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 C 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 211 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8272 (m-30) cc_final: 0.8041 (m-30) REVERT: A 335 GLN cc_start: 0.6608 (tt0) cc_final: 0.6388 (tm-30) REVERT: A 351 LYS cc_start: 0.7833 (ttmp) cc_final: 0.7587 (tptt) REVERT: B 82 LYS cc_start: 0.8701 (mttp) cc_final: 0.8252 (mttp) REVERT: B 329 VAL cc_start: 0.7944 (t) cc_final: 0.7599 (m) REVERT: B 360 MET cc_start: 0.8194 (tpt) cc_final: 0.7859 (tpt) REVERT: B 390 ASP cc_start: 0.7795 (m-30) cc_final: 0.7574 (m-30) REVERT: B 400 GLU cc_start: 0.6895 (tt0) cc_final: 0.6406 (mm-30) REVERT: C 325 ASP cc_start: 0.8252 (m-30) cc_final: 0.7984 (m-30) REVERT: C 351 LYS cc_start: 0.7809 (ttmp) cc_final: 0.7551 (tptt) REVERT: D 82 LYS cc_start: 0.8703 (mttp) cc_final: 0.8221 (mttp) REVERT: D 329 VAL cc_start: 0.8006 (t) cc_final: 0.7640 (m) REVERT: D 360 MET cc_start: 0.8184 (tpt) cc_final: 0.7834 (tpt) REVERT: D 400 GLU cc_start: 0.6909 (tt0) cc_final: 0.6397 (mm-30) outliers start: 15 outliers final: 10 residues processed: 205 average time/residue: 0.2845 time to fit residues: 81.0752 Evaluate side-chains 181 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN 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: 1.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7596 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12886 Z= 0.298 Angle : 0.704 10.414 17450 Z= 0.338 Chirality : 0.049 0.417 2034 Planarity : 0.005 0.055 2180 Dihedral : 11.955 76.938 2274 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.54 % Allowed : 9.25 % Favored : 88.21 % 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: -2.80 (0.21), residues: 1524 helix: -1.04 (0.19), residues: 608 sheet: -2.09 (0.29), residues: 332 loop : -2.45 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 353 HIS 0.007 0.001 HIS B 253 PHE 0.020 0.002 PHE A 107 TYR 0.021 0.002 TYR C 86 ARG 0.005 0.000 ARG A 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 218 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 LYS cc_start: 0.8752 (mttp) cc_final: 0.8388 (mttp) REVERT: B 160 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8054 (mt) REVERT: B 329 VAL cc_start: 0.7997 (t) cc_final: 0.7544 (m) REVERT: B 360 MET cc_start: 0.8189 (tpt) cc_final: 0.7734 (tpt) REVERT: B 361 SER cc_start: 0.7867 (m) cc_final: 0.7475 (p) REVERT: B 400 GLU cc_start: 0.6998 (tt0) cc_final: 0.6540 (mm-30) REVERT: C 351 LYS cc_start: 0.7818 (ttmp) cc_final: 0.7613 (tptt) REVERT: D 82 LYS cc_start: 0.8708 (mttp) cc_final: 0.8326 (mttp) REVERT: D 160 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.8008 (mt) REVERT: D 329 VAL cc_start: 0.7944 (t) cc_final: 0.7464 (m) REVERT: D 360 MET cc_start: 0.8183 (tpt) cc_final: 0.7717 (tpt) REVERT: D 361 SER cc_start: 0.7812 (m) cc_final: 0.7400 (p) REVERT: D 400 GLU cc_start: 0.7037 (tt0) cc_final: 0.6587 (mm-30) outliers start: 34 outliers final: 23 residues processed: 208 average time/residue: 0.2720 time to fit residues: 78.9476 Evaluate side-chains 195 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 378 ASN 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 238 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 THR 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 277 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 160 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 277 THR 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: 0.9980 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7593 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12886 Z= 0.255 Angle : 0.654 10.290 17450 Z= 0.314 Chirality : 0.048 0.396 2034 Planarity : 0.005 0.057 2180 Dihedral : 10.157 60.396 2274 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.31 % Allowed : 10.67 % Favored : 87.01 % 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: -2.23 (0.21), residues: 1524 helix: -0.28 (0.20), residues: 612 sheet: -1.92 (0.29), residues: 328 loop : -2.41 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 296 HIS 0.004 0.001 HIS B 253 PHE 0.017 0.002 PHE D 315 TYR 0.014 0.002 TYR A 146 ARG 0.004 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 205 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6978 (ptm160) REVERT: A 247 MET cc_start: 0.7483 (mmm) cc_final: 0.7217 (mmm) REVERT: B 82 LYS cc_start: 0.8716 (mttp) cc_final: 0.8351 (mttp) REVERT: B 160 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7988 (mt) REVERT: B 248 MET cc_start: 0.8550 (mmm) cc_final: 0.7932 (mmm) REVERT: B 329 VAL cc_start: 0.7949 (t) cc_final: 0.7499 (m) REVERT: B 360 MET cc_start: 0.8195 (tpt) cc_final: 0.7656 (tpt) REVERT: B 361 SER cc_start: 0.7835 (m) cc_final: 0.7454 (p) REVERT: B 400 GLU cc_start: 0.7022 (tt0) cc_final: 0.6543 (mm-30) REVERT: C 198 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7119 (ptm160) REVERT: D 82 LYS cc_start: 0.8716 (mttp) cc_final: 0.8342 (mttp) REVERT: D 160 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7956 (mt) REVERT: D 248 MET cc_start: 0.8556 (mmm) cc_final: 0.7923 (mmm) REVERT: D 329 VAL cc_start: 0.7973 (t) cc_final: 0.7504 (m) REVERT: D 361 SER cc_start: 0.7816 (m) cc_final: 0.7432 (p) REVERT: D 400 GLU cc_start: 0.7083 (tt0) cc_final: 0.6601 (mm-30) outliers start: 31 outliers final: 18 residues processed: 196 average time/residue: 0.2764 time to fit residues: 75.5320 Evaluate side-chains 183 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 262 PHE 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 277 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7634 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12886 Z= 0.329 Angle : 0.682 8.955 17450 Z= 0.327 Chirality : 0.048 0.383 2034 Planarity : 0.005 0.054 2180 Dihedral : 9.326 55.880 2274 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.91 % Allowed : 11.34 % Favored : 85.75 % 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: -2.02 (0.22), residues: 1524 helix: -0.05 (0.21), residues: 612 sheet: -1.91 (0.30), residues: 328 loop : -2.31 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 296 HIS 0.005 0.001 HIS D 232 PHE 0.019 0.002 PHE A 107 TYR 0.018 0.002 TYR A 44 ARG 0.003 0.000 ARG C 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 210 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7453 (mmm) cc_final: 0.7200 (mmm) REVERT: B 149 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8226 (mp) REVERT: B 160 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8057 (mt) REVERT: B 340 MET cc_start: 0.7986 (ttm) cc_final: 0.7698 (ttp) REVERT: B 361 SER cc_start: 0.7828 (m) cc_final: 0.7459 (p) REVERT: B 400 GLU cc_start: 0.7082 (tt0) cc_final: 0.6597 (mm-30) REVERT: C 294 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7276 (mm-30) REVERT: D 160 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8017 (mt) REVERT: D 340 MET cc_start: 0.7964 (ttm) cc_final: 0.7673 (ttp) REVERT: D 361 SER cc_start: 0.7805 (m) cc_final: 0.7378 (p) REVERT: D 400 GLU cc_start: 0.7089 (tt0) cc_final: 0.6598 (mm-30) outliers start: 39 outliers final: 28 residues processed: 205 average time/residue: 0.2745 time to fit residues: 79.1903 Evaluate side-chains 191 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 149 LEU 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 B residue 277 THR 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 277 THR Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 160 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 277 THR 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: 0.7980 chunk 132 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 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: 0.7576 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12886 Z= 0.174 Angle : 0.598 8.437 17450 Z= 0.286 Chirality : 0.045 0.356 2034 Planarity : 0.004 0.054 2180 Dihedral : 8.374 55.523 2274 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.39 % Allowed : 12.99 % Favored : 84.63 % 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: -1.58 (0.22), residues: 1524 helix: 0.35 (0.21), residues: 612 sheet: -1.66 (0.30), residues: 328 loop : -2.12 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.004 0.001 HIS A 253 PHE 0.016 0.001 PHE D 315 TYR 0.014 0.001 TYR A 146 ARG 0.004 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 207 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7412 (mmm) cc_final: 0.7157 (mmm) REVERT: B 82 LYS cc_start: 0.8760 (mttp) cc_final: 0.8368 (mttp) REVERT: B 194 ARG cc_start: 0.6614 (ptp90) cc_final: 0.6355 (ptt90) REVERT: B 329 VAL cc_start: 0.7909 (t) cc_final: 0.7415 (m) REVERT: B 340 MET cc_start: 0.7979 (ttm) cc_final: 0.7628 (ttp) REVERT: B 361 SER cc_start: 0.7852 (m) cc_final: 0.7483 (p) REVERT: B 400 GLU cc_start: 0.7020 (tt0) cc_final: 0.6565 (mm-30) REVERT: D 82 LYS cc_start: 0.8758 (mttp) cc_final: 0.8370 (mttp) REVERT: D 329 VAL cc_start: 0.7915 (t) cc_final: 0.7417 (m) REVERT: D 340 MET cc_start: 0.7981 (ttm) cc_final: 0.7620 (ttp) REVERT: D 361 SER cc_start: 0.7797 (m) cc_final: 0.7394 (p) REVERT: D 400 GLU cc_start: 0.7026 (tt0) cc_final: 0.6553 (mm-30) outliers start: 32 outliers final: 26 residues processed: 199 average time/residue: 0.2678 time to fit residues: 75.2144 Evaluate side-chains 193 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN 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 277 THR 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 201 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN 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 277 THR 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: 0.0970 chunk 16 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7579 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12886 Z= 0.191 Angle : 0.598 8.106 17450 Z= 0.285 Chirality : 0.045 0.355 2034 Planarity : 0.004 0.052 2180 Dihedral : 7.883 55.876 2274 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.09 % Allowed : 13.96 % Favored : 83.96 % 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: -1.29 (0.23), residues: 1524 helix: 0.60 (0.22), residues: 612 sheet: -1.51 (0.31), residues: 328 loop : -1.97 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.006 0.001 HIS A 232 PHE 0.018 0.001 PHE D 315 TYR 0.018 0.002 TYR C 44 ARG 0.004 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 196 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7469 (mmm) cc_final: 0.7221 (mmm) REVERT: B 82 LYS cc_start: 0.8778 (mttp) cc_final: 0.8373 (mttp) REVERT: B 329 VAL cc_start: 0.7901 (t) cc_final: 0.7403 (m) REVERT: B 340 MET cc_start: 0.8035 (ttm) cc_final: 0.7761 (ttp) REVERT: B 361 SER cc_start: 0.7850 (m) cc_final: 0.7470 (p) REVERT: B 400 GLU cc_start: 0.6993 (tt0) cc_final: 0.6556 (mm-30) REVERT: C 294 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7291 (mm-30) REVERT: D 82 LYS cc_start: 0.8785 (mttp) cc_final: 0.8385 (mttp) REVERT: D 329 VAL cc_start: 0.7905 (t) cc_final: 0.7404 (m) REVERT: D 340 MET cc_start: 0.8043 (ttm) cc_final: 0.7731 (ttp) REVERT: D 361 SER cc_start: 0.7809 (m) cc_final: 0.7427 (p) REVERT: D 400 GLU cc_start: 0.6980 (tt0) cc_final: 0.6545 (mm-30) outliers start: 28 outliers final: 25 residues processed: 188 average time/residue: 0.3031 time to fit residues: 77.8873 Evaluate side-chains 190 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 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 185 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 378 ASN 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 B residue 277 THR 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 277 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN 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 277 THR 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: 1.9990 chunk 87 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 339 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12886 Z= 0.214 Angle : 0.599 7.767 17450 Z= 0.288 Chirality : 0.045 0.349 2034 Planarity : 0.004 0.052 2180 Dihedral : 7.523 56.065 2274 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.69 % Allowed : 13.88 % Favored : 83.43 % 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: -1.17 (0.23), residues: 1524 helix: 0.71 (0.21), residues: 612 sheet: -1.49 (0.31), residues: 328 loop : -1.88 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.003 0.001 HIS A 253 PHE 0.018 0.001 PHE D 315 TYR 0.019 0.001 TYR B 195 ARG 0.004 0.000 ARG C 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 207 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7437 (mmm) cc_final: 0.7177 (mmm) REVERT: B 82 LYS cc_start: 0.8769 (mttp) cc_final: 0.8328 (mttp) REVERT: B 340 MET cc_start: 0.8037 (ttm) cc_final: 0.7814 (ttp) REVERT: B 361 SER cc_start: 0.7826 (m) cc_final: 0.7449 (p) REVERT: B 400 GLU cc_start: 0.7023 (tt0) cc_final: 0.6606 (mm-30) REVERT: C 294 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7387 (mm-30) REVERT: D 82 LYS cc_start: 0.8745 (mttp) cc_final: 0.8311 (mttp) REVERT: D 340 MET cc_start: 0.8032 (ttm) cc_final: 0.7785 (ttp) REVERT: D 361 SER cc_start: 0.7806 (m) cc_final: 0.7404 (p) REVERT: D 400 GLU cc_start: 0.7014 (tt0) cc_final: 0.6591 (mm-30) outliers start: 36 outliers final: 26 residues processed: 196 average time/residue: 0.2951 time to fit residues: 79.6561 Evaluate side-chains 187 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 378 ASN 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 B residue 277 THR 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 201 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 378 ASN 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 277 THR 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: 0.7980 chunk 140 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS C 165 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12886 Z= 0.232 Angle : 0.606 7.552 17450 Z= 0.292 Chirality : 0.045 0.343 2034 Planarity : 0.004 0.052 2180 Dihedral : 7.320 56.129 2274 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.16 % Allowed : 14.40 % Favored : 83.43 % 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: -1.10 (0.23), residues: 1524 helix: 0.75 (0.21), residues: 612 sheet: -1.45 (0.31), residues: 328 loop : -1.84 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 296 HIS 0.008 0.001 HIS C 232 PHE 0.018 0.001 PHE D 315 TYR 0.019 0.002 TYR C 44 ARG 0.004 0.000 ARG C 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 193 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 LYS cc_start: 0.8783 (mttp) cc_final: 0.8339 (mttp) REVERT: B 361 SER cc_start: 0.7841 (m) cc_final: 0.7468 (p) REVERT: B 400 GLU cc_start: 0.7023 (tt0) cc_final: 0.6613 (mm-30) REVERT: C 294 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7409 (mm-30) REVERT: D 82 LYS cc_start: 0.8767 (mttp) cc_final: 0.8316 (mttp) REVERT: D 340 MET cc_start: 0.8038 (ttm) cc_final: 0.7835 (ttp) REVERT: D 361 SER cc_start: 0.7807 (m) cc_final: 0.7403 (p) REVERT: D 400 GLU cc_start: 0.7004 (tt0) cc_final: 0.6596 (mm-30) outliers start: 29 outliers final: 27 residues processed: 185 average time/residue: 0.3094 time to fit residues: 78.2629 Evaluate side-chains 185 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 378 ASN 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 B residue 277 THR 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 201 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 378 ASN 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 277 THR 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: 0.9980 chunk 68 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12886 Z= 0.306 Angle : 0.647 7.573 17450 Z= 0.313 Chirality : 0.046 0.344 2034 Planarity : 0.004 0.052 2180 Dihedral : 7.333 56.345 2274 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.09 % Allowed : 14.93 % Favored : 82.99 % 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: -1.21 (0.22), residues: 1524 helix: 0.62 (0.21), residues: 612 sheet: -1.48 (0.31), residues: 328 loop : -1.85 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 296 HIS 0.005 0.001 HIS B 232 PHE 0.019 0.002 PHE D 315 TYR 0.016 0.002 TYR A 146 ARG 0.005 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 190 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7077 (mm-30) REVERT: B 361 SER cc_start: 0.7817 (m) cc_final: 0.7443 (p) REVERT: B 400 GLU cc_start: 0.7075 (tt0) cc_final: 0.6657 (mm-30) REVERT: C 294 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7445 (mm-30) REVERT: D 294 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7220 (mm-30) REVERT: D 361 SER cc_start: 0.7806 (m) cc_final: 0.7401 (p) REVERT: D 400 GLU cc_start: 0.7052 (tt0) cc_final: 0.6620 (mm-30) outliers start: 28 outliers final: 26 residues processed: 184 average time/residue: 0.2884 time to fit residues: 72.9946 Evaluate side-chains 183 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 378 ASN 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 B residue 277 THR 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 201 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain D residue 120 SER 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 277 THR 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: 0.0870 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 124 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 141 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN D 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.177180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144797 restraints weight = 12968.726| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.93 r_work: 0.3202 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4296 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= 0.174 Angle : 0.582 7.197 17450 Z= 0.282 Chirality : 0.044 0.332 2034 Planarity : 0.004 0.051 2180 Dihedral : 6.979 56.025 2274 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.39 % Allowed : 14.78 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1524 helix: 0.91 (0.21), residues: 612 sheet: -1.36 (0.31), residues: 328 loop : -1.68 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS A 253 PHE 0.018 0.001 PHE D 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: 3188.17 seconds wall clock time: 58 minutes 16.80 seconds (3496.80 seconds total)