Starting phenix.real_space_refine on Thu Feb 15 14:47:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwv_29520/02_2024/8fwv_29520.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwv_29520/02_2024/8fwv_29520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwv_29520/02_2024/8fwv_29520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwv_29520/02_2024/8fwv_29520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwv_29520/02_2024/8fwv_29520.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwv_29520/02_2024/8fwv_29520.pdb" } resolution = 3.03 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= 0.031 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 8004 2.51 5 N 2100 2.21 5 O 2412 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 ARG 68": "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 ARG 68": "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 ARG 68": "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 ARG 68": "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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12584 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: 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: "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: 6.96, per 1000 atoms: 0.55 Number of scatterers: 12584 At special positions: 0 Unit cell: (104, 160.576, 85.696, 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 2412 8.00 N 2100 7.00 C 8004 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 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 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: 5.17 Conformation dependent library (CDL) restraints added in 2.3 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, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.957A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.567A 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 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.525A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.664A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.630A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.957A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.567A 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 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.525A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.631A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.748A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.958A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 161 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.567A 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 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.597A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.526A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.630A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.747A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.958A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.567A 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 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.724A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.598A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.526A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.665A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.631A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY A 40 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS A 129 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG A 384 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.813A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 395 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY B 40 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU B 149 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLN B 131 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.813A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY C 40 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU C 149 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN C 131 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG C 384 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N SER C 148 " --> pdb=" O ARG C 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.812A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 43 removed outlier: 3.847A pdb=" N GLY D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 129 through 131 removed outlier: 6.464A pdb=" N HIS D 129 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU D 149 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLN D 131 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.812A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.626A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 392 through 395 428 hydrogen bonds defined for protein. 1236 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: 3.47 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3741 1.33 - 1.45: 2114 1.45 - 1.57: 6882 1.57 - 1.69: 7 1.69 - 1.81: 120 Bond restraints: 12864 Sorted by residual: bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.558 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.659 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.647 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.645 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.530 -0.124 2.00e-02 2.50e+03 3.81e+01 ... (remaining 12859 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.24: 354 106.24 - 113.18: 7082 113.18 - 120.12: 4295 120.12 - 127.06: 5532 127.06 - 134.00: 157 Bond angle restraints: 17420 Sorted by residual: angle pdb=" N THR B 414 " pdb=" CA THR B 414 " pdb=" C THR B 414 " ideal model delta sigma weight residual 112.88 107.59 5.29 1.29e+00 6.01e-01 1.68e+01 angle pdb=" N THR C 414 " pdb=" CA THR C 414 " pdb=" C THR C 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" N THR A 414 " pdb=" CA THR A 414 " pdb=" C THR A 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" N THR D 414 " pdb=" CA THR D 414 " pdb=" C THR D 414 " ideal model delta sigma weight residual 112.88 107.60 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " pdb=" C5 NAG D1002 " ideal model delta sigma weight residual 113.21 125.09 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 17415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 7718 23.14 - 46.27: 238 46.27 - 69.41: 48 69.41 - 92.54: 31 92.54 - 115.68: 25 Dihedral angle restraints: 8060 sinusoidal: 3592 harmonic: 4468 Sorted by residual: dihedral pdb=" CA GLY C 310 " pdb=" C GLY C 310 " pdb=" N LEU C 311 " pdb=" CA LEU C 311 " ideal model delta harmonic sigma weight residual -180.00 -119.43 -60.57 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLY A 310 " pdb=" C GLY A 310 " pdb=" N LEU A 311 " pdb=" CA LEU A 311 " ideal model delta harmonic sigma weight residual -180.00 -119.44 -60.56 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" N LEU B 311 " pdb=" CA LEU B 311 " ideal model delta harmonic sigma weight residual 180.00 -119.49 -60.51 0 5.00e+00 4.00e-02 1.46e+02 ... (remaining 8057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.373: 2018 0.373 - 0.747: 2 0.747 - 1.120: 0 1.120 - 1.493: 0 1.493 - 1.866: 4 Chirality restraints: 2024 Sorted by residual: 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 -0.53 -1.87 2.00e-01 2.50e+01 8.71e+01 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 275 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.60 -1.80 2.00e-01 2.50e+01 8.14e+01 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 275 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.16e+01 ... (remaining 2021 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 191 " -0.066 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO B 192 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 191 " 0.066 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO D 192 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 191 " -0.066 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO A 192 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.055 5.00e-02 4.00e+02 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4072 2.85 - 3.36: 10859 3.36 - 3.87: 20453 3.87 - 4.39: 23789 4.39 - 4.90: 41544 Nonbonded interactions: 100717 Sorted by model distance: nonbonded pdb=" OG1 THR A 173 " pdb=" OE1 GLU A 223 " model vdw 2.334 2.440 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLU B 223 " model vdw 2.334 2.440 nonbonded pdb=" OG1 THR D 173 " pdb=" OE1 GLU D 223 " model vdw 2.335 2.440 nonbonded pdb=" OG1 THR C 173 " pdb=" OE1 GLU C 223 " model vdw 2.335 2.440 nonbonded pdb=" OE1 GLU D 46 " pdb=" OG SER D 47 " model vdw 2.350 2.440 ... (remaining 100712 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 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' 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: 3.740 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: 15.260 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.360 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 0.152 12864 Z= 0.449 Angle : 1.066 11.876 17420 Z= 0.588 Chirality : 0.095 1.866 2024 Planarity : 0.008 0.100 2180 Dihedral : 14.818 115.681 5160 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.35 % Favored : 92.39 % Rotamer: Outliers : 1.19 % Allowed : 4.78 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.27 % 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: -5.20 (0.16), residues: 1524 helix: -4.16 (0.10), residues: 568 sheet: -2.50 (0.27), residues: 328 loop : -3.06 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A 353 HIS 0.010 0.002 HIS A 253 PHE 0.024 0.003 PHE A 107 TYR 0.016 0.002 TYR D 252 ARG 0.008 0.001 ARG D 158 *********************** 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 327 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 311 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8632 (m) cc_final: 0.8192 (p) REVERT: A 156 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 222 LYS cc_start: 0.7945 (mttm) cc_final: 0.7691 (mmtm) REVERT: A 262 PHE cc_start: 0.7324 (t80) cc_final: 0.7036 (p90) REVERT: A 291 SER cc_start: 0.7469 (t) cc_final: 0.7240 (m) REVERT: A 360 MET cc_start: 0.7834 (tpt) cc_final: 0.7147 (tpt) REVERT: B 262 PHE cc_start: 0.7190 (t80) cc_final: 0.6935 (p90) REVERT: B 267 GLU cc_start: 0.7154 (tp30) cc_final: 0.6951 (tp30) REVERT: B 351 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7860 (mppt) REVERT: B 360 MET cc_start: 0.8370 (tpt) cc_final: 0.8166 (tpt) REVERT: C 113 SER cc_start: 0.8636 (m) cc_final: 0.8201 (p) REVERT: C 156 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8297 (tp) REVERT: C 222 LYS cc_start: 0.7938 (mttm) cc_final: 0.7684 (mmtm) REVERT: C 262 PHE cc_start: 0.7303 (t80) cc_final: 0.7048 (p90) REVERT: C 291 SER cc_start: 0.7465 (t) cc_final: 0.7236 (m) REVERT: C 360 MET cc_start: 0.7832 (tpt) cc_final: 0.7148 (tpt) REVERT: D 152 ASP cc_start: 0.7924 (t0) cc_final: 0.7626 (t0) REVERT: D 198 ARG cc_start: 0.7350 (tmt-80) cc_final: 0.7052 (tpt90) REVERT: D 200 LYS cc_start: 0.7856 (mttp) cc_final: 0.7610 (mtpt) REVERT: D 247 MET cc_start: 0.9125 (mtp) cc_final: 0.8886 (mtp) REVERT: D 262 PHE cc_start: 0.7139 (t80) cc_final: 0.6876 (p90) REVERT: D 351 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7823 (mppt) outliers start: 16 outliers final: 4 residues processed: 325 average time/residue: 0.3093 time to fit residues: 134.7314 Evaluate side-chains 174 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 119 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 286 ASN A 335 GLN A 336 GLN A 346 GLN A 350 HIS B 288 GLN B 335 GLN B 336 GLN B 350 HIS C 196 ASN C 286 ASN C 335 GLN C 336 GLN C 346 GLN C 350 HIS D 288 GLN D 335 GLN D 336 GLN D 350 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12864 Z= 0.205 Angle : 0.707 10.354 17420 Z= 0.343 Chirality : 0.059 1.076 2024 Planarity : 0.006 0.081 2180 Dihedral : 12.831 84.502 2244 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.33 % Allowed : 9.33 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -3.80 (0.18), residues: 1524 helix: -2.29 (0.16), residues: 568 sheet: -2.36 (0.27), residues: 328 loop : -2.66 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 353 HIS 0.006 0.001 HIS D 253 PHE 0.020 0.002 PHE B 166 TYR 0.007 0.001 TYR D 195 ARG 0.005 0.000 ARG B 37 *********************** 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 232 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 174 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6831 (mm) REVERT: A 113 SER cc_start: 0.8650 (m) cc_final: 0.8233 (p) REVERT: A 156 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7845 (mt) REVERT: A 177 ASP cc_start: 0.7596 (t70) cc_final: 0.7373 (t0) REVERT: A 222 LYS cc_start: 0.7938 (mttm) cc_final: 0.7676 (mmtm) REVERT: A 262 PHE cc_start: 0.7365 (t80) cc_final: 0.7092 (p90) REVERT: A 291 SER cc_start: 0.7436 (t) cc_final: 0.7141 (m) REVERT: B 262 PHE cc_start: 0.7476 (t80) cc_final: 0.7079 (p90) REVERT: B 351 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7897 (mppt) REVERT: C 55 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6848 (mm) REVERT: C 113 SER cc_start: 0.8639 (m) cc_final: 0.8224 (p) REVERT: C 156 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7850 (mt) REVERT: C 177 ASP cc_start: 0.7586 (t70) cc_final: 0.7377 (t0) REVERT: C 222 LYS cc_start: 0.7939 (mttm) cc_final: 0.7674 (mmtm) REVERT: C 262 PHE cc_start: 0.7367 (t80) cc_final: 0.7096 (p90) REVERT: C 291 SER cc_start: 0.7421 (t) cc_final: 0.7131 (m) REVERT: D 198 ARG cc_start: 0.7318 (tmt-80) cc_final: 0.7016 (tpt90) REVERT: D 218 MET cc_start: 0.8809 (mtp) cc_final: 0.8514 (mtm) REVERT: D 247 MET cc_start: 0.9055 (mtp) cc_final: 0.8806 (mtp) REVERT: D 262 PHE cc_start: 0.7470 (t80) cc_final: 0.7006 (p90) REVERT: D 351 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7776 (mppt) outliers start: 58 outliers final: 34 residues processed: 212 average time/residue: 0.2616 time to fit residues: 78.8534 Evaluate side-chains 188 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 391 VAL 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: 3.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 346 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 346 GLN C 196 ASN C 346 GLN D 98 GLN D 165 GLN D 288 GLN D 346 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12864 Z= 0.345 Angle : 0.743 13.835 17420 Z= 0.352 Chirality : 0.060 1.095 2024 Planarity : 0.006 0.082 2180 Dihedral : 10.086 59.508 2244 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.78 % Allowed : 9.40 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -2.81 (0.19), residues: 1524 helix: -0.74 (0.19), residues: 576 sheet: -2.18 (0.27), residues: 332 loop : -2.69 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.010 0.001 HIS D 253 PHE 0.021 0.003 PHE D 377 TYR 0.014 0.002 TYR C 195 ARG 0.004 0.001 ARG B 384 *********************** 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 239 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 175 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6818 (mm) REVERT: A 113 SER cc_start: 0.8559 (m) cc_final: 0.8073 (p) REVERT: A 156 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7728 (mm) REVERT: A 160 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7967 (mp) REVERT: A 220 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7530 (mtm110) REVERT: A 222 LYS cc_start: 0.8035 (mttm) cc_final: 0.7711 (mmtm) REVERT: A 262 PHE cc_start: 0.7646 (t80) cc_final: 0.7025 (p90) REVERT: A 291 SER cc_start: 0.7562 (t) cc_final: 0.7233 (m) REVERT: A 381 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7577 (p0) REVERT: A 400 GLU cc_start: 0.6625 (tt0) cc_final: 0.6145 (mm-30) REVERT: B 55 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7758 (mm) REVERT: B 262 PHE cc_start: 0.7755 (t80) cc_final: 0.7125 (p90) REVERT: B 351 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7983 (mptt) REVERT: B 381 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7446 (p0) REVERT: C 55 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6835 (mm) REVERT: C 113 SER cc_start: 0.8549 (m) cc_final: 0.8062 (p) REVERT: C 156 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7735 (mm) REVERT: C 160 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7977 (mp) REVERT: C 220 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7531 (mtm110) REVERT: C 222 LYS cc_start: 0.8025 (mttm) cc_final: 0.7705 (mmtm) REVERT: C 262 PHE cc_start: 0.7632 (t80) cc_final: 0.7020 (p90) REVERT: C 291 SER cc_start: 0.7553 (t) cc_final: 0.7226 (m) REVERT: C 400 GLU cc_start: 0.6631 (tt0) cc_final: 0.6153 (mm-30) REVERT: D 50 MET cc_start: 0.7488 (ptp) cc_final: 0.7237 (ptt) REVERT: D 81 GLN cc_start: 0.8404 (mt0) cc_final: 0.8156 (mt0) REVERT: D 198 ARG cc_start: 0.7345 (tmt-80) cc_final: 0.7010 (tpt90) REVERT: D 218 MET cc_start: 0.8923 (mtp) cc_final: 0.8580 (mtm) REVERT: D 234 MET cc_start: 0.8292 (ttm) cc_final: 0.8080 (mtp) REVERT: D 247 MET cc_start: 0.9058 (mtp) cc_final: 0.8850 (mtp) REVERT: D 262 PHE cc_start: 0.7770 (t80) cc_final: 0.7098 (p90) REVERT: D 288 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7449 (mm-40) REVERT: D 351 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7881 (mppt) outliers start: 64 outliers final: 39 residues processed: 224 average time/residue: 0.2549 time to fit residues: 81.7276 Evaluate side-chains 205 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.0050 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.0070 chunk 146 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 overall best weight: 0.3012 ------------------------------------------------------------------------------- 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 288 GLN D 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12864 Z= 0.153 Angle : 0.640 12.596 17420 Z= 0.302 Chirality : 0.055 0.945 2024 Planarity : 0.005 0.077 2180 Dihedral : 8.675 56.376 2244 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.73 % Allowed : 11.34 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -2.15 (0.20), residues: 1524 helix: 0.23 (0.21), residues: 568 sheet: -2.02 (0.29), residues: 316 loop : -2.64 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 296 HIS 0.004 0.001 HIS C 253 PHE 0.011 0.001 PHE B 107 TYR 0.022 0.001 TYR C 195 ARG 0.002 0.000 ARG A 198 *********************** 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 213 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 163 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6699 (mm) REVERT: A 113 SER cc_start: 0.8560 (m) cc_final: 0.8065 (p) REVERT: A 160 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7831 (mp) REVERT: A 220 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7523 (mtm110) REVERT: A 222 LYS cc_start: 0.8005 (mttm) cc_final: 0.7700 (mmtm) REVERT: A 262 PHE cc_start: 0.7709 (t80) cc_final: 0.7013 (p90) REVERT: A 400 GLU cc_start: 0.6653 (tt0) cc_final: 0.6157 (mm-30) REVERT: B 50 MET cc_start: 0.7431 (ptp) cc_final: 0.7104 (ptt) REVERT: B 262 PHE cc_start: 0.7746 (t80) cc_final: 0.7100 (p90) REVERT: B 351 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7983 (mptt) REVERT: B 381 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7402 (p0) REVERT: C 55 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6691 (mm) REVERT: C 113 SER cc_start: 0.8538 (m) cc_final: 0.8042 (p) REVERT: C 160 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7879 (mp) REVERT: C 220 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7524 (mtm110) REVERT: C 222 LYS cc_start: 0.8008 (mttm) cc_final: 0.7707 (mmtm) REVERT: C 262 PHE cc_start: 0.7704 (t80) cc_final: 0.7017 (p90) REVERT: C 400 GLU cc_start: 0.6659 (tt0) cc_final: 0.6185 (mm-30) REVERT: D 81 GLN cc_start: 0.8309 (mt0) cc_final: 0.8109 (mt0) REVERT: D 218 MET cc_start: 0.8837 (mtp) cc_final: 0.8570 (mtm) REVERT: D 234 MET cc_start: 0.8252 (ttm) cc_final: 0.8014 (mtp) REVERT: D 247 MET cc_start: 0.9050 (mtp) cc_final: 0.8825 (mtp) REVERT: D 262 PHE cc_start: 0.7770 (t80) cc_final: 0.7103 (p90) REVERT: D 288 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7325 (mm-40) outliers start: 50 outliers final: 32 residues processed: 200 average time/residue: 0.2541 time to fit residues: 72.6860 Evaluate side-chains 192 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12864 Z= 0.300 Angle : 0.676 12.100 17420 Z= 0.316 Chirality : 0.049 0.971 2024 Planarity : 0.005 0.077 2180 Dihedral : 9.280 85.228 2240 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.48 % Allowed : 11.49 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.96 (0.21), residues: 1524 helix: 0.52 (0.21), residues: 568 sheet: -1.93 (0.28), residues: 336 loop : -2.67 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 296 HIS 0.012 0.001 HIS C 253 PHE 0.017 0.002 PHE B 107 TYR 0.014 0.002 TYR C 195 ARG 0.003 0.000 ARG B 384 *********************** 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 216 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 156 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6751 (mm) REVERT: A 113 SER cc_start: 0.8554 (m) cc_final: 0.8052 (p) REVERT: A 160 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 222 LYS cc_start: 0.8044 (mttm) cc_final: 0.7714 (mmtm) REVERT: A 262 PHE cc_start: 0.7849 (t80) cc_final: 0.7059 (p90) REVERT: A 400 GLU cc_start: 0.6679 (tt0) cc_final: 0.6182 (mm-30) REVERT: B 262 PHE cc_start: 0.7852 (t80) cc_final: 0.7134 (p90) REVERT: B 351 LYS cc_start: 0.8242 (mtmt) cc_final: 0.7970 (mppt) REVERT: B 381 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7435 (p0) REVERT: C 55 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6766 (mm) REVERT: C 160 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7908 (mp) REVERT: C 222 LYS cc_start: 0.8058 (mttm) cc_final: 0.7717 (mmtm) REVERT: C 262 PHE cc_start: 0.7847 (t80) cc_final: 0.7063 (p90) REVERT: C 283 ASN cc_start: 0.7063 (t0) cc_final: 0.6745 (t0) REVERT: C 400 GLU cc_start: 0.6681 (tt0) cc_final: 0.6186 (mm-30) REVERT: D 81 GLN cc_start: 0.8355 (mt0) cc_final: 0.8131 (mt0) REVERT: D 218 MET cc_start: 0.8876 (mtp) cc_final: 0.8584 (mtm) REVERT: D 234 MET cc_start: 0.8291 (ttm) cc_final: 0.8087 (mtp) REVERT: D 262 PHE cc_start: 0.7879 (t80) cc_final: 0.7066 (p90) REVERT: D 288 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7302 (mm-40) outliers start: 60 outliers final: 38 residues processed: 204 average time/residue: 0.2483 time to fit residues: 73.0237 Evaluate side-chains 194 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 98 GLN B 288 GLN C 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12864 Z= 0.199 Angle : 0.614 11.129 17420 Z= 0.289 Chirality : 0.046 0.881 2024 Planarity : 0.005 0.074 2180 Dihedral : 7.928 62.141 2240 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.10 % Allowed : 11.94 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.49 (0.21), residues: 1524 helix: 1.09 (0.22), residues: 576 sheet: -1.84 (0.28), residues: 312 loop : -2.54 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 296 HIS 0.004 0.001 HIS C 253 PHE 0.012 0.002 PHE D 107 TYR 0.017 0.001 TYR B 86 ARG 0.004 0.000 ARG A 220 *********************** 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 214 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 159 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6755 (mm) REVERT: A 113 SER cc_start: 0.8515 (m) cc_final: 0.8007 (p) REVERT: A 149 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8449 (mp) REVERT: A 160 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7801 (mp) REVERT: A 222 LYS cc_start: 0.7998 (mttm) cc_final: 0.7685 (mmtm) REVERT: A 262 PHE cc_start: 0.7848 (t80) cc_final: 0.7039 (p90) REVERT: A 283 ASN cc_start: 0.7110 (t0) cc_final: 0.6827 (t0) REVERT: A 400 GLU cc_start: 0.6674 (tt0) cc_final: 0.6180 (mm-30) REVERT: B 149 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8297 (mt) REVERT: B 200 LYS cc_start: 0.7987 (mttp) cc_final: 0.7719 (mttt) REVERT: B 262 PHE cc_start: 0.7978 (t80) cc_final: 0.7168 (p90) REVERT: B 351 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7970 (mppt) REVERT: B 381 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7405 (p0) REVERT: C 55 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6767 (mm) REVERT: C 149 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8448 (mp) REVERT: C 160 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7810 (mp) REVERT: C 222 LYS cc_start: 0.8010 (mttm) cc_final: 0.7692 (mmtm) REVERT: C 262 PHE cc_start: 0.7845 (t80) cc_final: 0.7039 (p90) REVERT: C 283 ASN cc_start: 0.7127 (t0) cc_final: 0.6848 (t0) REVERT: C 400 GLU cc_start: 0.6673 (tt0) cc_final: 0.6184 (mm-30) REVERT: D 81 GLN cc_start: 0.8306 (mt0) cc_final: 0.8093 (mt0) REVERT: D 200 LYS cc_start: 0.8003 (mttp) cc_final: 0.7686 (mttt) REVERT: D 218 MET cc_start: 0.8874 (mtp) cc_final: 0.8615 (mtm) REVERT: D 234 MET cc_start: 0.8241 (ttm) cc_final: 0.8029 (mtp) REVERT: D 262 PHE cc_start: 0.7971 (t80) cc_final: 0.7094 (p90) REVERT: D 288 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7316 (mm-40) outliers start: 55 outliers final: 33 residues processed: 203 average time/residue: 0.2472 time to fit residues: 72.4918 Evaluate side-chains 198 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 HIS B 288 GLN D 225 HIS D 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12864 Z= 0.317 Angle : 0.648 10.829 17420 Z= 0.310 Chirality : 0.049 0.958 2024 Planarity : 0.005 0.075 2180 Dihedral : 7.326 48.650 2240 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.73 % Allowed : 12.84 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.54 (0.21), residues: 1524 helix: 1.00 (0.22), residues: 576 sheet: -1.79 (0.29), residues: 312 loop : -2.57 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.005 0.001 HIS D 232 PHE 0.021 0.002 PHE A 107 TYR 0.029 0.002 TYR B 86 ARG 0.003 0.000 ARG D 384 *********************** 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 212 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7073 (mt) REVERT: A 149 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8493 (mp) REVERT: A 160 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7914 (mp) REVERT: A 222 LYS cc_start: 0.7978 (mttm) cc_final: 0.7675 (mmtm) REVERT: A 262 PHE cc_start: 0.7986 (t80) cc_final: 0.7141 (p90) REVERT: A 400 GLU cc_start: 0.6684 (tt0) cc_final: 0.6188 (mm-30) REVERT: B 200 LYS cc_start: 0.8067 (mttp) cc_final: 0.7736 (mttt) REVERT: B 262 PHE cc_start: 0.8155 (t80) cc_final: 0.7241 (p90) REVERT: B 351 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7863 (mppt) REVERT: C 55 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7086 (mt) REVERT: C 149 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 160 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7930 (mp) REVERT: C 222 LYS cc_start: 0.7996 (mttm) cc_final: 0.7683 (mmtm) REVERT: C 262 PHE cc_start: 0.7965 (t80) cc_final: 0.7100 (p90) REVERT: C 400 GLU cc_start: 0.6681 (tt0) cc_final: 0.6195 (mm-30) REVERT: D 50 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7346 (ptt) REVERT: D 81 GLN cc_start: 0.8328 (mt0) cc_final: 0.8099 (mt0) REVERT: D 149 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8306 (mt) REVERT: D 200 LYS cc_start: 0.8054 (mttp) cc_final: 0.7683 (mttt) REVERT: D 218 MET cc_start: 0.8889 (mtp) cc_final: 0.8564 (mtm) REVERT: D 262 PHE cc_start: 0.8174 (t80) cc_final: 0.7160 (p90) REVERT: D 288 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7388 (mm-40) outliers start: 50 outliers final: 38 residues processed: 200 average time/residue: 0.2548 time to fit residues: 73.2464 Evaluate side-chains 204 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12864 Z= 0.224 Angle : 0.579 9.435 17420 Z= 0.281 Chirality : 0.046 0.842 2024 Planarity : 0.005 0.074 2180 Dihedral : 6.920 55.370 2240 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.51 % Allowed : 12.69 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.36 (0.21), residues: 1524 helix: 1.30 (0.22), residues: 572 sheet: -1.96 (0.34), residues: 228 loop : -2.46 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 296 HIS 0.004 0.001 HIS A 253 PHE 0.015 0.002 PHE A 107 TYR 0.018 0.001 TYR B 86 ARG 0.002 0.000 ARG D 58 *********************** 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 208 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7030 (mt) REVERT: A 113 SER cc_start: 0.8398 (m) cc_final: 0.7853 (p) REVERT: A 149 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 160 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7814 (mp) REVERT: A 222 LYS cc_start: 0.7934 (mttm) cc_final: 0.7646 (mmtm) REVERT: A 262 PHE cc_start: 0.7956 (t80) cc_final: 0.7163 (p90) REVERT: A 400 GLU cc_start: 0.6660 (tt0) cc_final: 0.6183 (mm-30) REVERT: B 50 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7115 (ptt) REVERT: B 149 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8296 (mt) REVERT: B 200 LYS cc_start: 0.8034 (mttp) cc_final: 0.7823 (mttt) REVERT: B 262 PHE cc_start: 0.8214 (t80) cc_final: 0.7241 (p90) REVERT: B 351 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7777 (mppt) REVERT: C 55 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7044 (mt) REVERT: C 149 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8462 (mp) REVERT: C 160 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7825 (mp) REVERT: C 222 LYS cc_start: 0.7948 (mttm) cc_final: 0.7652 (mmtm) REVERT: C 262 PHE cc_start: 0.7957 (t80) cc_final: 0.7163 (p90) REVERT: C 351 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7805 (mptt) REVERT: C 400 GLU cc_start: 0.6667 (tt0) cc_final: 0.6192 (mm-30) REVERT: D 50 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7059 (ptt) REVERT: D 81 GLN cc_start: 0.8292 (mt0) cc_final: 0.8088 (mt0) REVERT: D 149 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8252 (mt) REVERT: D 200 LYS cc_start: 0.8010 (mttp) cc_final: 0.7641 (mttt) REVERT: D 218 MET cc_start: 0.8877 (mtp) cc_final: 0.8623 (mtm) REVERT: D 262 PHE cc_start: 0.8225 (t80) cc_final: 0.7152 (p90) REVERT: D 288 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7368 (mm-40) outliers start: 47 outliers final: 37 residues processed: 196 average time/residue: 0.2465 time to fit residues: 69.8132 Evaluate side-chains 206 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 336 GLN B 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12864 Z= 0.232 Angle : 0.587 9.629 17420 Z= 0.285 Chirality : 0.046 0.854 2024 Planarity : 0.005 0.074 2180 Dihedral : 6.863 59.580 2240 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.88 % Allowed : 12.16 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.30 (0.21), residues: 1524 helix: 1.37 (0.22), residues: 572 sheet: -1.95 (0.34), residues: 228 loop : -2.43 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 296 HIS 0.007 0.001 HIS B 350 PHE 0.015 0.002 PHE B 107 TYR 0.021 0.001 TYR B 86 ARG 0.002 0.000 ARG B 58 *********************** 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 216 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 164 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7055 (mt) REVERT: A 149 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8481 (mp) REVERT: A 160 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 196 ASN cc_start: 0.7628 (t0) cc_final: 0.7363 (t0) REVERT: A 210 ASP cc_start: 0.7444 (p0) cc_final: 0.7241 (p0) REVERT: A 222 LYS cc_start: 0.7938 (mttm) cc_final: 0.7652 (mmtm) REVERT: A 262 PHE cc_start: 0.8016 (t80) cc_final: 0.7186 (p90) REVERT: A 400 GLU cc_start: 0.6635 (tt0) cc_final: 0.6145 (mm-30) REVERT: B 50 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.7032 (ptt) REVERT: B 149 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8303 (mt) REVERT: B 200 LYS cc_start: 0.8014 (mttp) cc_final: 0.7661 (mttt) REVERT: B 234 MET cc_start: 0.8320 (ttm) cc_final: 0.8118 (mtp) REVERT: B 262 PHE cc_start: 0.8208 (t80) cc_final: 0.7204 (p90) REVERT: B 351 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7859 (mptt) REVERT: C 55 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7069 (mt) REVERT: C 149 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 160 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7867 (mp) REVERT: C 196 ASN cc_start: 0.7623 (t0) cc_final: 0.7361 (t0) REVERT: C 222 LYS cc_start: 0.7952 (mttm) cc_final: 0.7657 (mmtm) REVERT: C 262 PHE cc_start: 0.8004 (t80) cc_final: 0.7171 (p90) REVERT: C 351 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7744 (mptt) REVERT: C 400 GLU cc_start: 0.6654 (tt0) cc_final: 0.6176 (mm-30) REVERT: D 50 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7044 (ptt) REVERT: D 81 GLN cc_start: 0.8283 (mt0) cc_final: 0.8078 (mt0) REVERT: D 149 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8265 (mt) REVERT: D 200 LYS cc_start: 0.8017 (mttp) cc_final: 0.7641 (mttt) REVERT: D 218 MET cc_start: 0.8881 (mtp) cc_final: 0.8588 (mtm) REVERT: D 262 PHE cc_start: 0.8215 (t80) cc_final: 0.7137 (p90) REVERT: D 288 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7373 (mm-40) outliers start: 52 outliers final: 39 residues processed: 203 average time/residue: 0.2502 time to fit residues: 72.9731 Evaluate side-chains 211 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 0.0570 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 95 optimal weight: 0.0170 chunk 128 optimal weight: 2.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12864 Z= 0.160 Angle : 0.547 8.026 17420 Z= 0.267 Chirality : 0.045 0.769 2024 Planarity : 0.004 0.074 2180 Dihedral : 6.439 50.262 2240 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.51 % Allowed : 12.84 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.08 (0.21), residues: 1524 helix: 1.62 (0.22), residues: 572 sheet: -1.91 (0.34), residues: 228 loop : -2.34 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 296 HIS 0.006 0.001 HIS B 350 PHE 0.011 0.001 PHE D 107 TYR 0.022 0.001 TYR B 86 ARG 0.002 0.000 ARG D 58 ********************** 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 208 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7053 (mt) REVERT: A 149 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8470 (mp) REVERT: A 160 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7860 (mp) REVERT: A 196 ASN cc_start: 0.7593 (t0) cc_final: 0.7327 (t0) REVERT: A 222 LYS cc_start: 0.7921 (mttm) cc_final: 0.7638 (mmtm) REVERT: A 262 PHE cc_start: 0.8028 (t80) cc_final: 0.7232 (p90) REVERT: A 283 ASN cc_start: 0.7085 (t0) cc_final: 0.6816 (t0) REVERT: A 400 GLU cc_start: 0.6608 (tt0) cc_final: 0.6128 (mm-30) REVERT: B 50 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6861 (ptt) REVERT: B 149 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8288 (mt) REVERT: B 200 LYS cc_start: 0.7915 (mttp) cc_final: 0.7587 (mttt) REVERT: B 234 MET cc_start: 0.8292 (ttm) cc_final: 0.8079 (mtp) REVERT: B 262 PHE cc_start: 0.8176 (t80) cc_final: 0.7177 (p90) REVERT: B 351 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7801 (mppt) REVERT: C 55 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7073 (mt) REVERT: C 149 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8470 (mp) REVERT: C 160 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7873 (mp) REVERT: C 196 ASN cc_start: 0.7592 (t0) cc_final: 0.7320 (t0) REVERT: C 222 LYS cc_start: 0.7928 (mttm) cc_final: 0.7632 (mmtm) REVERT: C 262 PHE cc_start: 0.8020 (t80) cc_final: 0.7232 (p90) REVERT: C 283 ASN cc_start: 0.7104 (t0) cc_final: 0.6834 (t0) REVERT: C 351 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7824 (mptt) REVERT: C 400 GLU cc_start: 0.6633 (tt0) cc_final: 0.6148 (mm-30) REVERT: D 50 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6906 (ptt) REVERT: D 149 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8241 (mt) REVERT: D 200 LYS cc_start: 0.7953 (mttp) cc_final: 0.7580 (mttt) REVERT: D 218 MET cc_start: 0.8838 (mtp) cc_final: 0.8611 (mtm) REVERT: D 262 PHE cc_start: 0.8177 (t80) cc_final: 0.7105 (p90) REVERT: D 288 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7364 (mm-40) outliers start: 47 outliers final: 33 residues processed: 194 average time/residue: 0.2503 time to fit residues: 70.1757 Evaluate side-chains 197 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN B 288 GLN C 165 GLN D 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.171106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131561 restraints weight = 13402.491| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.36 r_work: 0.3255 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12864 Z= 0.261 Angle : 0.595 9.024 17420 Z= 0.290 Chirality : 0.047 0.811 2024 Planarity : 0.005 0.074 2180 Dihedral : 6.506 48.979 2240 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.66 % Allowed : 12.46 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.16 (0.21), residues: 1524 helix: 1.47 (0.22), residues: 572 sheet: -1.89 (0.34), residues: 228 loop : -2.34 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 296 HIS 0.006 0.001 HIS B 350 PHE 0.016 0.002 PHE B 107 TYR 0.026 0.002 TYR D 86 ARG 0.002 0.000 ARG D 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.19 seconds wall clock time: 58 minutes 12.41 seconds (3492.41 seconds total)