Starting phenix.real_space_refine on Thu Feb 15 15:09:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwr_29516/02_2024/8fwr_29516.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwr_29516/02_2024/8fwr_29516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwr_29516/02_2024/8fwr_29516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwr_29516/02_2024/8fwr_29516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwr_29516/02_2024/8fwr_29516.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwr_29516/02_2024/8fwr_29516.pdb" } resolution = 3.1 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= 0.002 sd= 0.107 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 8028 2.51 5 N 2100 2.21 5 O 2432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 58": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12628 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 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: 7.31, per 1000 atoms: 0.58 Number of scatterers: 12628 At special positions: 0 Unit cell: (165.575, 102.675, 84.175, 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 2432 8.00 N 2100 7.00 C 8028 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=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.04 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " 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: 5.62 Conformation dependent library (CDL) restraints added in 2.9 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: 52 helices and 20 sheets defined 40.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.951A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.918A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (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 191 through 194 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.594A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.580A pdb=" N SER A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.952A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.919A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (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 191 through 194 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.594A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU B 264 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.579A pdb=" N SER B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.951A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.919A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (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 191 through 194 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.593A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU C 264 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.580A pdb=" N SER C 297 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.951A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.919A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (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 191 through 194 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.671A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.594A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 removed outlier: 3.552A pdb=" N LEU D 264 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.579A pdb=" N SER D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.558A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 43 removed outlier: 6.398A pdb=" N HIS A 34 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 77 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.865A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.562A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA6, first strand: chain 'B' and resid 34 through 43 removed outlier: 6.398A pdb=" N HIS B 34 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR B 77 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 7.866A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.563A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AB2, first strand: chain 'C' and resid 34 through 43 removed outlier: 6.398A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.866A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.562A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 373 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AB7, first strand: chain 'D' and resid 34 through 43 removed outlier: 6.399A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'D' and resid 202 through 203 removed outlier: 7.866A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.563A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 392 through 394 404 hydrogen bonds defined for protein. 1188 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: 3.32 Time building geometry restraints manager: 6.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3887 1.34 - 1.46: 2223 1.46 - 1.57: 6669 1.57 - 1.69: 9 1.69 - 1.81: 120 Bond restraints: 12908 Sorted by residual: bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.536 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C ALA A 191 " pdb=" N PRO A 192 " ideal model delta sigma weight residual 1.337 1.387 -0.050 9.80e-03 1.04e+04 2.62e+01 bond pdb=" C ALA D 191 " pdb=" N PRO D 192 " ideal model delta sigma weight residual 1.337 1.386 -0.050 9.80e-03 1.04e+04 2.55e+01 bond pdb=" C ALA B 191 " pdb=" N PRO B 192 " ideal model delta sigma weight residual 1.337 1.386 -0.049 9.80e-03 1.04e+04 2.51e+01 ... (remaining 12903 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.05: 239 105.05 - 112.29: 6446 112.29 - 119.53: 4270 119.53 - 126.77: 6333 126.77 - 134.01: 192 Bond angle restraints: 17480 Sorted by residual: angle pdb=" C ASN B 84 " pdb=" N LEU B 85 " pdb=" CA LEU B 85 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C ASN A 84 " pdb=" N LEU A 85 " pdb=" CA LEU A 85 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASN D 84 " pdb=" N LEU D 85 " pdb=" CA LEU D 85 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C ASN C 84 " pdb=" N LEU C 85 " pdb=" CA LEU C 85 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N VAL A 266 " pdb=" CA VAL A 266 " pdb=" C VAL A 266 " ideal model delta sigma weight residual 112.29 108.15 4.14 9.40e-01 1.13e+00 1.94e+01 ... (remaining 17475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.46: 7698 24.46 - 48.92: 224 48.92 - 73.37: 97 73.37 - 97.83: 83 97.83 - 122.29: 34 Dihedral angle restraints: 8136 sinusoidal: 3668 harmonic: 4468 Sorted by residual: dihedral pdb=" CA GLY C 246 " pdb=" C GLY C 246 " pdb=" N MET C 247 " pdb=" CA MET C 247 " ideal model delta harmonic sigma weight residual -180.00 -139.86 -40.14 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" CA GLY A 246 " pdb=" C GLY A 246 " pdb=" N MET A 247 " pdb=" CA MET A 247 " ideal model delta harmonic sigma weight residual 180.00 -139.86 -40.14 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" CA GLY B 246 " pdb=" C GLY B 246 " pdb=" N MET B 247 " pdb=" CA MET B 247 " ideal model delta harmonic sigma weight residual -180.00 -139.87 -40.13 0 5.00e+00 4.00e-02 6.44e+01 ... (remaining 8133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1954 0.118 - 0.235: 66 0.235 - 0.353: 18 0.353 - 0.470: 2 0.470 - 0.587: 4 Chirality restraints: 2044 Sorted by residual: chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 412 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 412 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.36e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 67 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.95e+00 ... (remaining 2041 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 67 " -0.034 2.00e-02 2.50e+03 3.49e-02 1.53e+01 pdb=" CG ASN A 67 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 67 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 67 " 0.052 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 67 " 0.034 2.00e-02 2.50e+03 3.40e-02 1.45e+01 pdb=" CG ASN C 67 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 67 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 67 " -0.050 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 275 " 0.000 2.00e-02 2.50e+03 2.97e-02 1.11e+01 pdb=" CG ASN C 275 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN C 275 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN C 275 " -0.050 2.00e-02 2.50e+03 pdb=" C1 NAG C1001 " 0.033 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4104 2.85 - 3.36: 11074 3.36 - 3.87: 20440 3.87 - 4.39: 23830 4.39 - 4.90: 41134 Nonbonded interactions: 100582 Sorted by model distance: nonbonded pdb=" OD1 ASN C 378 " pdb=" OG1 THR C 385 " model vdw 2.334 2.440 nonbonded pdb=" OD1 ASN A 378 " pdb=" OG1 THR A 385 " model vdw 2.335 2.440 nonbonded pdb=" OD1 ASN D 378 " pdb=" OG1 THR D 385 " model vdw 2.335 2.440 nonbonded pdb=" OD1 ASN B 378 " pdb=" OG1 THR B 385 " model vdw 2.335 2.440 nonbonded pdb=" ND2 ASN C 123 " pdb=" OD1 ASP C 143 " model vdw 2.401 2.520 ... (remaining 100577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 3.320 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: 13.130 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.630 Find NCS groups from input model: 0.790 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 : 0.008 0.142 12908 Z= 0.496 Angle : 1.100 13.091 17480 Z= 0.609 Chirality : 0.066 0.587 2044 Planarity : 0.007 0.069 2180 Dihedral : 19.319 122.290 5236 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.74 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -5.62 (0.14), residues: 1524 helix: -4.07 (0.09), residues: 580 sheet: -3.43 (0.25), residues: 304 loop : -3.33 (0.18), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 353 HIS 0.009 0.002 HIS D 111 PHE 0.023 0.003 PHE B 359 TYR 0.014 0.002 TYR B 146 ARG 0.010 0.001 ARG A 58 *********************** 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 325 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.7965 (mttp) cc_final: 0.7704 (mtmt) REVERT: A 234 MET cc_start: 0.6886 (mtp) cc_final: 0.6643 (mtt) REVERT: B 55 LEU cc_start: 0.7187 (mm) cc_final: 0.6838 (mp) REVERT: B 84 ASN cc_start: 0.7593 (t0) cc_final: 0.7244 (t0) REVERT: B 154 SER cc_start: 0.8195 (m) cc_final: 0.7961 (m) REVERT: B 240 LYS cc_start: 0.7578 (mttm) cc_final: 0.7350 (mtpp) REVERT: B 262 PHE cc_start: 0.6866 (t80) cc_final: 0.6518 (p90) REVERT: B 267 GLU cc_start: 0.7583 (tt0) cc_final: 0.7351 (tm-30) REVERT: B 271 TYR cc_start: 0.7148 (m-80) cc_final: 0.6842 (m-80) REVERT: B 296 TRP cc_start: 0.7670 (t-100) cc_final: 0.7324 (t-100) REVERT: B 316 MET cc_start: 0.7898 (mtm) cc_final: 0.7652 (mtt) REVERT: B 361 SER cc_start: 0.8025 (t) cc_final: 0.7715 (p) REVERT: C 78 TYR cc_start: 0.6914 (p90) cc_final: 0.6572 (p90) REVERT: C 170 LYS cc_start: 0.7981 (mttp) cc_final: 0.7715 (mtmt) REVERT: C 234 MET cc_start: 0.6903 (mtp) cc_final: 0.6561 (mtt) REVERT: C 323 MET cc_start: 0.8580 (tpp) cc_final: 0.8377 (tpp) REVERT: C 360 MET cc_start: 0.8172 (tpt) cc_final: 0.7621 (tpt) REVERT: D 55 LEU cc_start: 0.7406 (mm) cc_final: 0.7128 (mp) REVERT: D 144 SER cc_start: 0.8092 (p) cc_final: 0.7799 (t) REVERT: D 200 LYS cc_start: 0.7387 (mttp) cc_final: 0.7091 (ttmt) REVERT: D 240 LYS cc_start: 0.7724 (mttm) cc_final: 0.7493 (mtpp) REVERT: D 262 PHE cc_start: 0.7036 (t80) cc_final: 0.6664 (p90) REVERT: D 296 TRP cc_start: 0.7762 (t-100) cc_final: 0.7418 (t-100) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.3028 time to fit residues: 132.8897 Evaluate side-chains 182 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 138 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 288 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 288 GLN D 84 ASN D 137 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12908 Z= 0.232 Angle : 0.746 15.829 17480 Z= 0.348 Chirality : 0.050 0.404 2044 Planarity : 0.006 0.063 2180 Dihedral : 18.140 89.408 2312 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.77 % Favored : 94.16 % Rotamer: Outliers : 2.09 % Allowed : 8.21 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.86 (0.18), residues: 1524 helix: -1.84 (0.17), residues: 604 sheet: -2.97 (0.26), residues: 308 loop : -2.92 (0.21), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 353 HIS 0.008 0.001 HIS D 253 PHE 0.016 0.001 PHE C 228 TYR 0.017 0.001 TYR A 252 ARG 0.007 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8041 (mttp) cc_final: 0.7747 (mtmt) REVERT: A 234 MET cc_start: 0.6124 (mtp) cc_final: 0.5856 (mtt) REVERT: A 312 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6660 (mp) REVERT: A 360 MET cc_start: 0.8199 (tpt) cc_final: 0.7952 (tpt) REVERT: B 35 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8155 (m) REVERT: B 82 LYS cc_start: 0.8527 (mmtp) cc_final: 0.7986 (mmtm) REVERT: B 240 LYS cc_start: 0.7186 (mttm) cc_final: 0.6939 (mtpp) REVERT: B 262 PHE cc_start: 0.6862 (t80) cc_final: 0.6381 (p90) REVERT: B 288 GLN cc_start: 0.6820 (tp-100) cc_final: 0.6364 (mp10) REVERT: B 361 SER cc_start: 0.7872 (t) cc_final: 0.7507 (p) REVERT: C 170 LYS cc_start: 0.8024 (mttp) cc_final: 0.7702 (mtmt) REVERT: C 234 MET cc_start: 0.6098 (mtp) cc_final: 0.5784 (mtt) REVERT: C 250 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: C 312 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6698 (mp) REVERT: D 35 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8217 (p) REVERT: D 240 LYS cc_start: 0.7301 (mttm) cc_final: 0.7058 (mtpp) REVERT: D 262 PHE cc_start: 0.7017 (t80) cc_final: 0.6506 (p90) REVERT: D 286 ASN cc_start: 0.7423 (t0) cc_final: 0.7150 (t0) REVERT: D 288 GLN cc_start: 0.7000 (tp-100) cc_final: 0.6482 (mp10) REVERT: D 296 TRP cc_start: 0.7802 (t-100) cc_final: 0.7423 (t-100) outliers start: 28 outliers final: 10 residues processed: 220 average time/residue: 0.2619 time to fit residues: 81.4205 Evaluate side-chains 179 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 357 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 137 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN B 84 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12908 Z= 0.248 Angle : 0.690 10.361 17480 Z= 0.319 Chirality : 0.049 0.301 2044 Planarity : 0.005 0.059 2180 Dihedral : 13.632 86.210 2312 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.23 % Favored : 93.64 % Rotamer: Outliers : 2.54 % Allowed : 8.73 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.50 (0.20), residues: 1524 helix: -0.28 (0.20), residues: 600 sheet: -2.81 (0.26), residues: 312 loop : -2.31 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 353 HIS 0.005 0.001 HIS A 253 PHE 0.019 0.002 PHE C 337 TYR 0.014 0.001 TYR B 86 ARG 0.007 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8109 (mttp) cc_final: 0.7800 (mtmt) REVERT: A 234 MET cc_start: 0.6201 (mtp) cc_final: 0.5946 (mtt) REVERT: A 360 MET cc_start: 0.8091 (tpt) cc_final: 0.7870 (tpt) REVERT: B 35 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8128 (p) REVERT: B 82 LYS cc_start: 0.8569 (mmtp) cc_final: 0.8003 (mmtm) REVERT: B 240 LYS cc_start: 0.7189 (mttm) cc_final: 0.6949 (mtpp) REVERT: B 248 MET cc_start: 0.8747 (mmm) cc_final: 0.8338 (mmm) REVERT: B 262 PHE cc_start: 0.7216 (t80) cc_final: 0.6377 (p90) REVERT: B 335 GLN cc_start: 0.6937 (tt0) cc_final: 0.6670 (tt0) REVERT: B 361 SER cc_start: 0.7781 (t) cc_final: 0.7400 (p) REVERT: C 170 LYS cc_start: 0.8089 (mttp) cc_final: 0.7806 (mtmt) REVERT: C 234 MET cc_start: 0.6171 (mtp) cc_final: 0.5877 (mtt) REVERT: C 245 MET cc_start: 0.7196 (mtp) cc_final: 0.6898 (ttm) REVERT: C 250 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: C 251 TYR cc_start: 0.6491 (m-80) cc_final: 0.6173 (m-80) REVERT: D 35 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8342 (m) REVERT: D 262 PHE cc_start: 0.7301 (t80) cc_final: 0.6615 (p90) REVERT: D 286 ASN cc_start: 0.7502 (t0) cc_final: 0.7044 (t0) REVERT: D 288 GLN cc_start: 0.6819 (tp-100) cc_final: 0.6460 (mp10) outliers start: 34 outliers final: 15 residues processed: 191 average time/residue: 0.2573 time to fit residues: 70.0075 Evaluate side-chains 168 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 350 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.6980 chunk 103 optimal weight: 0.0050 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 136 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12908 Z= 0.210 Angle : 0.636 8.464 17480 Z= 0.293 Chirality : 0.045 0.268 2044 Planarity : 0.005 0.061 2180 Dihedral : 12.137 130.334 2312 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.62 % Rotamer: Outliers : 2.69 % Allowed : 9.55 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.21), residues: 1524 helix: 0.68 (0.21), residues: 600 sheet: -2.49 (0.27), residues: 304 loop : -2.06 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS C 253 PHE 0.017 0.001 PHE C 337 TYR 0.021 0.001 TYR A 44 ARG 0.005 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8066 (mttp) cc_final: 0.7772 (mtmt) REVERT: A 198 ARG cc_start: 0.7155 (ttt-90) cc_final: 0.6946 (tpt170) REVERT: A 234 MET cc_start: 0.6160 (mtp) cc_final: 0.5907 (mtt) REVERT: A 248 MET cc_start: 0.7678 (mmm) cc_final: 0.7406 (mmm) REVERT: B 35 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8118 (p) REVERT: B 82 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8021 (mmtm) REVERT: B 85 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6986 (mp) REVERT: B 240 LYS cc_start: 0.7154 (mttm) cc_final: 0.6946 (mtpp) REVERT: B 262 PHE cc_start: 0.7344 (t80) cc_final: 0.6392 (p90) REVERT: B 271 TYR cc_start: 0.7760 (m-80) cc_final: 0.7228 (m-80) REVERT: B 361 SER cc_start: 0.7757 (t) cc_final: 0.7355 (p) REVERT: C 170 LYS cc_start: 0.8087 (mttp) cc_final: 0.7790 (mtmt) REVERT: C 234 MET cc_start: 0.6094 (mtp) cc_final: 0.5808 (mtt) REVERT: C 251 TYR cc_start: 0.6598 (m-80) cc_final: 0.6232 (m-80) REVERT: D 35 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8362 (m) REVERT: D 262 PHE cc_start: 0.7438 (t80) cc_final: 0.6648 (p90) outliers start: 36 outliers final: 15 residues processed: 174 average time/residue: 0.2630 time to fit residues: 66.7670 Evaluate side-chains 162 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 350 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 0.0010 chunk 60 optimal weight: 0.0980 chunk 125 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12908 Z= 0.196 Angle : 0.602 8.163 17480 Z= 0.279 Chirality : 0.044 0.236 2044 Planarity : 0.004 0.058 2180 Dihedral : 10.979 126.987 2312 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.75 % Rotamer: Outliers : 1.94 % Allowed : 10.22 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.18 (0.22), residues: 1524 helix: 1.18 (0.22), residues: 600 sheet: -2.28 (0.28), residues: 304 loop : -1.93 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS A 253 PHE 0.013 0.001 PHE C 337 TYR 0.014 0.001 TYR C 44 ARG 0.007 0.000 ARG A 66 *********************** 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 177 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8075 (mttp) cc_final: 0.7831 (mtmt) REVERT: A 198 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6230 (ttp-170) REVERT: A 234 MET cc_start: 0.6237 (mtp) cc_final: 0.5986 (mtt) REVERT: B 82 LYS cc_start: 0.8557 (mmtp) cc_final: 0.8029 (mmtm) REVERT: B 85 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7021 (mp) REVERT: B 240 LYS cc_start: 0.7102 (mttm) cc_final: 0.6863 (mtpp) REVERT: B 262 PHE cc_start: 0.7498 (t80) cc_final: 0.6489 (p90) REVERT: B 271 TYR cc_start: 0.7806 (m-80) cc_final: 0.7348 (m-80) REVERT: B 361 SER cc_start: 0.7720 (t) cc_final: 0.7308 (p) REVERT: C 154 SER cc_start: 0.7357 (m) cc_final: 0.7118 (p) REVERT: C 170 LYS cc_start: 0.8088 (mttp) cc_final: 0.7800 (mtmt) REVERT: C 234 MET cc_start: 0.6155 (mtp) cc_final: 0.5847 (mtt) REVERT: C 247 MET cc_start: 0.7412 (mmm) cc_final: 0.7201 (mmm) REVERT: C 251 TYR cc_start: 0.6631 (m-80) cc_final: 0.6242 (m-80) REVERT: D 35 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8349 (m) REVERT: D 241 GLN cc_start: 0.7853 (mt0) cc_final: 0.7607 (mt0) REVERT: D 262 PHE cc_start: 0.7489 (t80) cc_final: 0.6649 (p90) REVERT: D 348 ASN cc_start: 0.7844 (p0) cc_final: 0.7631 (p0) outliers start: 26 outliers final: 15 residues processed: 171 average time/residue: 0.2512 time to fit residues: 62.8149 Evaluate side-chains 159 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 350 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.0870 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12908 Z= 0.271 Angle : 0.623 7.503 17480 Z= 0.292 Chirality : 0.045 0.251 2044 Planarity : 0.005 0.066 2180 Dihedral : 10.515 126.793 2312 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.36 % Favored : 93.50 % Rotamer: Outliers : 2.46 % Allowed : 10.75 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.06 (0.22), residues: 1524 helix: 1.20 (0.22), residues: 600 sheet: -2.13 (0.28), residues: 304 loop : -1.84 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.004 0.001 HIS D 232 PHE 0.011 0.001 PHE C 337 TYR 0.015 0.001 TYR C 44 ARG 0.003 0.000 ARG A 66 *********************** 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 187 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8068 (mttp) cc_final: 0.7807 (mtmt) REVERT: A 234 MET cc_start: 0.6431 (mtp) cc_final: 0.6125 (mtt) REVERT: B 82 LYS cc_start: 0.8558 (mmtp) cc_final: 0.8026 (mmtm) REVERT: B 85 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7215 (mp) REVERT: B 240 LYS cc_start: 0.7112 (mttm) cc_final: 0.6910 (mtpp) REVERT: B 262 PHE cc_start: 0.7697 (t80) cc_final: 0.6532 (p90) REVERT: B 271 TYR cc_start: 0.7845 (m-80) cc_final: 0.7513 (m-80) REVERT: B 335 GLN cc_start: 0.6967 (tt0) cc_final: 0.6677 (tt0) REVERT: B 361 SER cc_start: 0.7780 (t) cc_final: 0.7297 (p) REVERT: B 400 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7079 (mt-10) REVERT: C 154 SER cc_start: 0.7462 (m) cc_final: 0.7245 (p) REVERT: C 170 LYS cc_start: 0.8035 (mttp) cc_final: 0.7777 (mtmt) REVERT: C 234 MET cc_start: 0.6398 (mtp) cc_final: 0.6030 (mtt) REVERT: C 245 MET cc_start: 0.7210 (mtp) cc_final: 0.6935 (ttm) REVERT: C 251 TYR cc_start: 0.6604 (m-80) cc_final: 0.6141 (m-80) REVERT: D 35 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8450 (m) REVERT: D 241 GLN cc_start: 0.7847 (mt0) cc_final: 0.7590 (mt0) REVERT: D 262 PHE cc_start: 0.7708 (t80) cc_final: 0.6677 (p90) REVERT: D 315 PHE cc_start: 0.6959 (p90) cc_final: 0.5290 (m-80) outliers start: 33 outliers final: 20 residues processed: 180 average time/residue: 0.2343 time to fit residues: 61.8148 Evaluate side-chains 168 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 350 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.0000 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12908 Z= 0.187 Angle : 0.586 7.256 17480 Z= 0.274 Chirality : 0.044 0.237 2044 Planarity : 0.005 0.061 2180 Dihedral : 9.860 125.840 2312 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 1.94 % Allowed : 11.42 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1524 helix: 1.48 (0.22), residues: 600 sheet: -1.99 (0.29), residues: 304 loop : -1.72 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS A 253 PHE 0.009 0.001 PHE B 359 TYR 0.015 0.001 TYR A 44 ARG 0.008 0.000 ARG D 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8058 (mttp) cc_final: 0.7788 (mtmt) REVERT: A 234 MET cc_start: 0.6361 (mtp) cc_final: 0.6056 (mtt) REVERT: B 82 LYS cc_start: 0.8488 (mmtp) cc_final: 0.7965 (mmtm) REVERT: B 171 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.7069 (m) REVERT: B 240 LYS cc_start: 0.7109 (mttm) cc_final: 0.6908 (mtpp) REVERT: B 262 PHE cc_start: 0.7745 (t80) cc_final: 0.6529 (p90) REVERT: B 271 TYR cc_start: 0.7819 (m-80) cc_final: 0.7473 (m-80) REVERT: B 315 PHE cc_start: 0.6940 (p90) cc_final: 0.5214 (m-80) REVERT: B 335 GLN cc_start: 0.6921 (tt0) cc_final: 0.6622 (tt0) REVERT: B 361 SER cc_start: 0.7763 (t) cc_final: 0.7282 (p) REVERT: C 154 SER cc_start: 0.7474 (m) cc_final: 0.7267 (p) REVERT: C 170 LYS cc_start: 0.8029 (mttp) cc_final: 0.7750 (mtmt) REVERT: C 234 MET cc_start: 0.6350 (mtp) cc_final: 0.6008 (mtt) REVERT: C 245 MET cc_start: 0.7076 (mtp) cc_final: 0.6793 (ttm) REVERT: C 251 TYR cc_start: 0.6417 (m-80) cc_final: 0.6018 (m-80) REVERT: D 35 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8479 (m) REVERT: D 241 GLN cc_start: 0.7837 (mt0) cc_final: 0.7584 (mt0) REVERT: D 262 PHE cc_start: 0.7802 (t80) cc_final: 0.6695 (p90) REVERT: D 315 PHE cc_start: 0.6912 (p90) cc_final: 0.5280 (m-80) outliers start: 26 outliers final: 18 residues processed: 171 average time/residue: 0.2422 time to fit residues: 61.5374 Evaluate side-chains 171 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12908 Z= 0.254 Angle : 0.609 7.091 17480 Z= 0.286 Chirality : 0.045 0.247 2044 Planarity : 0.005 0.065 2180 Dihedral : 9.524 124.928 2312 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.36 % Favored : 93.50 % Rotamer: Outliers : 2.01 % Allowed : 11.19 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1524 helix: 1.39 (0.22), residues: 600 sheet: -1.95 (0.29), residues: 304 loop : -1.66 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.004 0.001 HIS D 232 PHE 0.010 0.001 PHE A 337 TYR 0.016 0.001 TYR C 44 ARG 0.006 0.000 ARG D 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6996 (p90) cc_final: 0.6490 (p90) REVERT: A 170 LYS cc_start: 0.8049 (mttp) cc_final: 0.7795 (mtmt) REVERT: A 234 MET cc_start: 0.6484 (mtp) cc_final: 0.6166 (mtt) REVERT: A 248 MET cc_start: 0.7584 (mmm) cc_final: 0.7359 (mmm) REVERT: B 82 LYS cc_start: 0.8451 (mmtp) cc_final: 0.7925 (mmtm) REVERT: B 171 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7263 (m) REVERT: B 240 LYS cc_start: 0.7171 (mttm) cc_final: 0.6955 (mtpp) REVERT: B 262 PHE cc_start: 0.7892 (t80) cc_final: 0.6535 (p90) REVERT: B 271 TYR cc_start: 0.7914 (m-80) cc_final: 0.7625 (m-80) REVERT: B 315 PHE cc_start: 0.6953 (p90) cc_final: 0.5211 (m-80) REVERT: B 335 GLN cc_start: 0.6923 (tt0) cc_final: 0.6643 (tt0) REVERT: B 361 SER cc_start: 0.7753 (t) cc_final: 0.7278 (p) REVERT: C 78 TYR cc_start: 0.7122 (p90) cc_final: 0.6525 (p90) REVERT: C 154 SER cc_start: 0.7535 (m) cc_final: 0.7334 (p) REVERT: C 170 LYS cc_start: 0.8065 (mttp) cc_final: 0.7789 (mtmt) REVERT: C 234 MET cc_start: 0.6484 (mtp) cc_final: 0.6112 (mtt) REVERT: C 245 MET cc_start: 0.7007 (mtp) cc_final: 0.6741 (ttm) REVERT: C 251 TYR cc_start: 0.6505 (m-80) cc_final: 0.6026 (m-80) REVERT: C 267 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7004 (mm-30) REVERT: C 349 ARG cc_start: 0.7546 (mpt180) cc_final: 0.7241 (mpt-90) REVERT: D 241 GLN cc_start: 0.7851 (mt0) cc_final: 0.7586 (mt0) REVERT: D 262 PHE cc_start: 0.7946 (t80) cc_final: 0.6693 (p90) REVERT: D 315 PHE cc_start: 0.6943 (p90) cc_final: 0.5338 (m-80) outliers start: 27 outliers final: 19 residues processed: 178 average time/residue: 0.2418 time to fit residues: 63.3490 Evaluate side-chains 174 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 140 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12908 Z= 0.228 Angle : 0.594 6.970 17480 Z= 0.282 Chirality : 0.044 0.261 2044 Planarity : 0.005 0.064 2180 Dihedral : 9.097 123.875 2312 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.77 % Favored : 94.09 % Rotamer: Outliers : 1.64 % Allowed : 12.09 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1524 helix: 1.42 (0.22), residues: 604 sheet: -1.81 (0.29), residues: 304 loop : -1.70 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS B 232 PHE 0.036 0.001 PHE A 337 TYR 0.015 0.001 TYR A 44 ARG 0.002 0.000 ARG A 66 *********************** 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 181 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7058 (p90) cc_final: 0.6487 (p90) REVERT: A 170 LYS cc_start: 0.8061 (mttp) cc_final: 0.7785 (mtmt) REVERT: A 234 MET cc_start: 0.6483 (mtp) cc_final: 0.6165 (mtt) REVERT: A 248 MET cc_start: 0.7585 (mmm) cc_final: 0.7299 (mmm) REVERT: B 82 LYS cc_start: 0.8430 (mmtp) cc_final: 0.7905 (mmtm) REVERT: B 171 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7272 (m) REVERT: B 240 LYS cc_start: 0.7166 (mttm) cc_final: 0.6960 (mtpp) REVERT: B 251 TYR cc_start: 0.8065 (m-80) cc_final: 0.7864 (m-80) REVERT: B 262 PHE cc_start: 0.8003 (t80) cc_final: 0.6594 (p90) REVERT: B 271 TYR cc_start: 0.7922 (m-80) cc_final: 0.7680 (m-80) REVERT: B 335 GLN cc_start: 0.6983 (tt0) cc_final: 0.6683 (tt0) REVERT: B 361 SER cc_start: 0.7765 (t) cc_final: 0.7267 (p) REVERT: B 400 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7087 (mt-10) REVERT: C 78 TYR cc_start: 0.7106 (p90) cc_final: 0.6430 (p90) REVERT: C 170 LYS cc_start: 0.8053 (mttp) cc_final: 0.7792 (mtmt) REVERT: C 234 MET cc_start: 0.6454 (mtp) cc_final: 0.6102 (mtt) REVERT: C 251 TYR cc_start: 0.6462 (m-80) cc_final: 0.5986 (m-80) REVERT: C 349 ARG cc_start: 0.7543 (mpt180) cc_final: 0.7239 (mpt-90) REVERT: D 241 GLN cc_start: 0.7874 (mt0) cc_final: 0.7640 (mt0) REVERT: D 262 PHE cc_start: 0.8006 (t80) cc_final: 0.6720 (p90) REVERT: D 315 PHE cc_start: 0.6958 (p90) cc_final: 0.5341 (m-80) outliers start: 22 outliers final: 16 residues processed: 176 average time/residue: 0.2453 time to fit residues: 63.0587 Evaluate side-chains 171 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12908 Z= 0.248 Angle : 0.604 6.805 17480 Z= 0.286 Chirality : 0.044 0.242 2044 Planarity : 0.005 0.065 2180 Dihedral : 8.844 123.064 2312 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.30 % Favored : 93.57 % Rotamer: Outliers : 1.27 % Allowed : 12.76 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.22), residues: 1524 helix: 1.42 (0.22), residues: 604 sheet: -1.72 (0.30), residues: 304 loop : -1.70 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS D 232 PHE 0.022 0.001 PHE A 337 TYR 0.016 0.001 TYR C 44 ARG 0.010 0.000 ARG D 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7108 (p90) cc_final: 0.6471 (p90) REVERT: A 170 LYS cc_start: 0.8042 (mttp) cc_final: 0.7783 (mtmt) REVERT: A 234 MET cc_start: 0.6521 (mtp) cc_final: 0.6189 (mtt) REVERT: A 248 MET cc_start: 0.7586 (mmm) cc_final: 0.7327 (mmm) REVERT: A 337 PHE cc_start: 0.7541 (t80) cc_final: 0.7188 (t80) REVERT: B 82 LYS cc_start: 0.8447 (mmtp) cc_final: 0.7909 (mmtm) REVERT: B 248 MET cc_start: 0.8829 (mtp) cc_final: 0.8571 (mtm) REVERT: B 262 PHE cc_start: 0.8037 (t80) cc_final: 0.6581 (p90) REVERT: B 335 GLN cc_start: 0.7009 (tt0) cc_final: 0.6722 (tt0) REVERT: B 361 SER cc_start: 0.7756 (t) cc_final: 0.7261 (p) REVERT: B 400 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7104 (mt-10) REVERT: C 78 TYR cc_start: 0.7128 (p90) cc_final: 0.6473 (p90) REVERT: C 170 LYS cc_start: 0.8056 (mttp) cc_final: 0.7796 (mtmt) REVERT: C 234 MET cc_start: 0.6519 (mtp) cc_final: 0.6155 (mtt) REVERT: C 245 MET cc_start: 0.6761 (ttm) cc_final: 0.6439 (mtp) REVERT: C 251 TYR cc_start: 0.6464 (m-80) cc_final: 0.5948 (m-80) REVERT: C 349 ARG cc_start: 0.7655 (mpt180) cc_final: 0.7348 (mpt-90) REVERT: D 241 GLN cc_start: 0.7875 (mt0) cc_final: 0.7624 (mt0) REVERT: D 262 PHE cc_start: 0.8040 (t80) cc_final: 0.6725 (p90) REVERT: D 315 PHE cc_start: 0.6993 (p90) cc_final: 0.5372 (m-80) outliers start: 17 outliers final: 15 residues processed: 168 average time/residue: 0.2402 time to fit residues: 59.1101 Evaluate side-chains 167 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.0370 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.169651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126977 restraints weight = 12902.751| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.46 r_work: 0.3338 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12908 Z= 0.174 Angle : 0.576 8.468 17480 Z= 0.272 Chirality : 0.043 0.228 2044 Planarity : 0.004 0.062 2180 Dihedral : 8.413 122.538 2312 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.75 % Rotamer: Outliers : 1.19 % Allowed : 13.13 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1524 helix: 1.66 (0.22), residues: 604 sheet: -1.61 (0.30), residues: 304 loop : -1.65 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 296 HIS 0.004 0.001 HIS B 253 PHE 0.026 0.001 PHE A 337 TYR 0.015 0.001 TYR A 44 ARG 0.003 0.000 ARG D 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.10 seconds wall clock time: 51 minutes 28.45 seconds (3088.45 seconds total)