Starting phenix.real_space_refine on Sun Mar 17 07:28:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qko_14048/03_2024/7qko_14048_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qko_14048/03_2024/7qko_14048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qko_14048/03_2024/7qko_14048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qko_14048/03_2024/7qko_14048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qko_14048/03_2024/7qko_14048_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qko_14048/03_2024/7qko_14048_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.061 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 85 5.16 5 C 11150 2.51 5 N 2615 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17042 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3210 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3218 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 373} Chain breaks: 1 Chain: "C" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3408 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 392} Chain breaks: 1 Chain: "D" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3089 Classifications: {'peptide': 380} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "E" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3278 Classifications: {'peptide': 404} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 382} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "L" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Time building chain proxies: 8.93, per 1000 atoms: 0.52 Number of scatterers: 17042 At special positions: 0 Unit cell: (103.05, 106.485, 172.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 8 15.00 O 3184 8.00 N 2615 7.00 C 11150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 7 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 7 " " MAN L 4 " - " MAN L 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 6 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 6 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 6 " BETA1-4 " 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 F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 141 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN C 70 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 141 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 2.7 seconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3854 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 25 sheets defined 38.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.302A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.793A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 Processing helix chain 'A' and resid 273 through 299 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 371 through 433 removed outlier: 4.087A pdb=" N ILE A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 218 through 240 removed outlier: 4.940A pdb=" N ILE B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 4.298A pdb=" N PHE B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 268 removed outlier: 4.094A pdb=" N SER B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 306 Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.888A pdb=" N ILE B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 411 through 460 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 233 through 247 removed outlier: 3.558A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 277 removed outlier: 3.941A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 313 Processing helix chain 'C' and resid 324 through 337 Proline residue: C 335 - end of helix Processing helix chain 'C' and resid 423 through 477 Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 212 through 229 removed outlier: 4.960A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'D' and resid 273 through 299 Processing helix chain 'D' and resid 310 through 323 Proline residue: D 321 - end of helix Processing helix chain 'D' and resid 382 through 430 removed outlier: 3.710A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG D 429 " --> pdb=" O VAL D 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 132 through 134 No H-bonds generated for 'chain 'E' and resid 132 through 134' Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 227 through 241 removed outlier: 3.897A pdb=" N LEU E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 272 removed outlier: 3.767A pdb=" N LYS E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 309 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 417 through 472 removed outlier: 3.590A pdb=" N ASN E 439 " --> pdb=" O SER E 435 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP E 440 " --> pdb=" O GLU E 436 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS E 471 " --> pdb=" O PHE E 467 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.022A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'A' and resid 58 through 61 Processing sheet with id= D, first strand: chain 'A' and resid 77 through 81 Processing sheet with id= E, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.452A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.375A pdb=" N VAL B 29 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLN B 159 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 31 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 42 through 44 Processing sheet with id= H, first strand: chain 'B' and resid 58 through 61 Processing sheet with id= I, first strand: chain 'B' and resid 77 through 80 Processing sheet with id= J, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= K, first strand: chain 'B' and resid 186 through 190 removed outlier: 6.805A pdb=" N ILE B 212 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.554A pdb=" N VAL C 31 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 33 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 32 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR C 63 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN C 55 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= N, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.945A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 164 through 166 Processing sheet with id= P, first strand: chain 'D' and resid 156 through 160 removed outlier: 6.617A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= R, first strand: chain 'D' and resid 58 through 61 Processing sheet with id= S, first strand: chain 'D' and resid 77 through 80 Processing sheet with id= T, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.694A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.793A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= W, first strand: chain 'E' and resid 77 through 81 Processing sheet with id= X, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.828A pdb=" N CYS E 142 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.952A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2610 1.31 - 1.43: 4824 1.43 - 1.56: 9872 1.56 - 1.68: 27 1.68 - 1.81: 138 Bond restraints: 17471 Sorted by residual: bond pdb=" C31 POV C 601 " pdb=" O31 POV C 601 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C31 POV A 502 " pdb=" O31 POV A 502 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C31 POV C 603 " pdb=" O31 POV C 603 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C31 POV C 602 " pdb=" O31 POV C 602 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C31 POV A 501 " pdb=" O31 POV A 501 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.33e+01 ... (remaining 17466 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.85: 674 106.85 - 113.64: 10188 113.64 - 120.42: 6315 120.42 - 127.21: 6360 127.21 - 134.00: 245 Bond angle restraints: 23782 Sorted by residual: angle pdb=" O13 POV C 602 " pdb=" P POV C 602 " pdb=" O14 POV C 602 " ideal model delta sigma weight residual 121.11 109.29 11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O13 POV D 501 " pdb=" P POV D 501 " pdb=" O14 POV D 501 " ideal model delta sigma weight residual 121.11 109.31 11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O11 POV D 501 " pdb=" P POV D 501 " pdb=" O12 POV D 501 " ideal model delta sigma weight residual 97.67 109.44 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O13 POV A 501 " pdb=" P POV A 501 " pdb=" O14 POV A 501 " ideal model delta sigma weight residual 121.11 109.43 11.68 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O11 POV A 501 " pdb=" P POV A 501 " pdb=" O12 POV A 501 " ideal model delta sigma weight residual 97.67 109.32 -11.65 3.00e+00 1.11e-01 1.51e+01 ... (remaining 23777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 10456 31.27 - 62.53: 334 62.53 - 93.80: 77 93.80 - 125.07: 54 125.07 - 156.34: 7 Dihedral angle restraints: 10928 sinusoidal: 5007 harmonic: 5921 Sorted by residual: dihedral pdb=" C3 POV C 603 " pdb=" C31 POV C 603 " pdb=" O31 POV C 603 " pdb=" C32 POV C 603 " ideal model delta sinusoidal sigma weight residual 172.61 16.27 156.34 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C3 POV A 501 " pdb=" C31 POV A 501 " pdb=" O31 POV A 501 " pdb=" C32 POV A 501 " ideal model delta sinusoidal sigma weight residual 172.61 -40.50 -146.89 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C3 POV B 501 " pdb=" C31 POV B 501 " pdb=" O31 POV B 501 " pdb=" C32 POV B 501 " ideal model delta sinusoidal sigma weight residual 172.61 -41.14 -146.25 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 10925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2387 0.060 - 0.119: 400 0.119 - 0.179: 46 0.179 - 0.239: 4 0.239 - 0.299: 6 Chirality restraints: 2843 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2840 not shown) Planarity restraints: 2863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 119 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO E 120 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 120 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 120 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 291 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C MET E 291 " 0.029 2.00e-02 2.50e+03 pdb=" O MET E 291 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE E 292 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 316 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C PHE D 316 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE D 316 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE D 317 " 0.009 2.00e-02 2.50e+03 ... (remaining 2860 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3111 2.77 - 3.31: 16481 3.31 - 3.84: 28698 3.84 - 4.37: 33598 4.37 - 4.90: 57935 Nonbonded interactions: 139823 Sorted by model distance: nonbonded pdb=" OD1 ASN E 68 " pdb=" OG SER E 70 " model vdw 2.242 2.440 nonbonded pdb=" O LEU E 92 " pdb=" ND2 ASN E 95 " model vdw 2.254 2.520 nonbonded pdb=" O ILE A 315 " pdb=" OG1 THR A 319 " model vdw 2.257 2.440 nonbonded pdb=" OD1 ASN B 107 " pdb=" ND2 ASN C 152 " model vdw 2.268 2.520 nonbonded pdb=" O GLY A 153 " pdb=" OG1 THR A 154 " model vdw 2.278 2.440 ... (remaining 139818 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' and (resid 1 through 328 or resid 381 through 432 or (resid 501 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name O11 or name O12 or name O13 or n \ ame O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid 5 \ 02 and (name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or n \ ame C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name O21 or name O22 or name O \ 31 or name O32)))) selection = (chain 'D' and (resid 1 through 432 or resid 501 or (resid 502 and (name C2 or n \ ame C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name O21 or name O22 or name O31 or name O32)))) } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) selection = (chain 'K' and (resid 2 or resid 5 through 7)) selection = (chain 'L' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.45 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.610 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 44.350 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 0.006 0.103 17471 Z= 0.401 Angle : 0.845 11.825 23782 Z= 0.348 Chirality : 0.047 0.299 2843 Planarity : 0.004 0.045 2856 Dihedral : 18.352 156.336 7059 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.25 % Allowed : 5.42 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1976 helix: 1.85 (0.19), residues: 745 sheet: -0.76 (0.25), residues: 408 loop : -1.01 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 187 HIS 0.004 0.001 HIS E 471 PHE 0.010 0.001 PHE A 284 TYR 0.008 0.001 TYR C 439 ARG 0.002 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 311 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7824 (pt0) cc_final: 0.7529 (pt0) REVERT: A 324 MET cc_start: 0.8341 (mtm) cc_final: 0.7944 (mtm) REVERT: B 48 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7879 (mt-10) REVERT: B 93 MET cc_start: 0.8248 (mmm) cc_final: 0.7804 (mmt) REVERT: B 177 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7796 (tmtp) REVERT: B 268 ASP cc_start: 0.7838 (m-30) cc_final: 0.7114 (m-30) REVERT: B 275 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8130 (mt) REVERT: B 285 MET cc_start: 0.7745 (mmt) cc_final: 0.7343 (mmt) REVERT: C 5 GLU cc_start: 0.7199 (pt0) cc_final: 0.6742 (tt0) REVERT: C 46 LYS cc_start: 0.7172 (tttp) cc_final: 0.6695 (mtpt) REVERT: C 49 ASP cc_start: 0.7831 (m-30) cc_final: 0.7403 (m-30) REVERT: C 186 GLU cc_start: 0.7809 (tt0) cc_final: 0.7544 (tp30) REVERT: C 280 GLU cc_start: 0.7752 (mp0) cc_final: 0.7140 (mt-10) REVERT: D 45 GLU cc_start: 0.8205 (mp0) cc_final: 0.7956 (mp0) REVERT: D 94 ASN cc_start: 0.7990 (m110) cc_final: 0.7517 (m110) REVERT: D 105 MET cc_start: 0.8637 (mmt) cc_final: 0.8305 (mmt) REVERT: D 163 ASP cc_start: 0.7105 (t0) cc_final: 0.6731 (t0) REVERT: D 171 MET cc_start: 0.7413 (mtm) cc_final: 0.7130 (mtt) REVERT: D 172 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7784 (mp0) REVERT: D 320 ILE cc_start: 0.6325 (mm) cc_final: 0.6061 (mm) REVERT: D 398 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6489 (tp30) REVERT: E 44 ASN cc_start: 0.7182 (t0) cc_final: 0.6540 (t0) REVERT: E 48 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7751 (mt-10) REVERT: E 93 GLU cc_start: 0.7426 (tp30) cc_final: 0.6980 (tp30) REVERT: E 166 GLU cc_start: 0.7121 (pt0) cc_final: 0.6807 (pt0) REVERT: E 225 ASN cc_start: 0.8138 (m-40) cc_final: 0.7931 (m110) REVERT: E 469 THR cc_start: 0.8270 (m) cc_final: 0.8025 (p) REVERT: E 474 GLN cc_start: 0.7323 (pt0) cc_final: 0.7010 (mt0) outliers start: 23 outliers final: 4 residues processed: 329 average time/residue: 1.0085 time to fit residues: 378.2047 Evaluate side-chains 201 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 280 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN C 152 ASN D 14 ASN D 58 GLN E 39 ASN E 53 ASN E 107 ASN E 196 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17471 Z= 0.173 Angle : 0.553 8.496 23782 Z= 0.263 Chirality : 0.044 0.246 2843 Planarity : 0.004 0.041 2856 Dihedral : 18.902 138.677 3208 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.31 % Allowed : 12.04 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1976 helix: 2.00 (0.19), residues: 754 sheet: -0.71 (0.25), residues: 402 loop : -0.93 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 187 HIS 0.003 0.001 HIS D 204 PHE 0.012 0.001 PHE C 473 TYR 0.013 0.001 TYR C 117 ARG 0.004 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 223 time to evaluate : 1.873 Fit side-chains revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7755 (pt0) cc_final: 0.7478 (pt0) REVERT: A 262 GLU cc_start: 0.7668 (tt0) cc_final: 0.7396 (tt0) REVERT: A 324 MET cc_start: 0.8119 (mtm) cc_final: 0.7693 (mtm) REVERT: A 407 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: B 93 MET cc_start: 0.8251 (mmm) cc_final: 0.7759 (mmt) REVERT: B 167 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6336 (pm20) REVERT: B 177 LYS cc_start: 0.8043 (tmtt) cc_final: 0.7841 (tmtp) REVERT: B 268 ASP cc_start: 0.7915 (m-30) cc_final: 0.7395 (m-30) REVERT: B 275 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8132 (mt) REVERT: B 285 MET cc_start: 0.7700 (mmt) cc_final: 0.7300 (mmt) REVERT: C 5 GLU cc_start: 0.7199 (pt0) cc_final: 0.6735 (tt0) REVERT: C 46 LYS cc_start: 0.7186 (tttp) cc_final: 0.6978 (mtpp) REVERT: C 186 GLU cc_start: 0.7783 (tt0) cc_final: 0.7540 (tp30) REVERT: C 280 GLU cc_start: 0.7652 (mp0) cc_final: 0.7106 (mt-10) REVERT: C 489 ASP cc_start: 0.7885 (t70) cc_final: 0.7630 (t0) REVERT: D 13 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: D 89 ASP cc_start: 0.7281 (m-30) cc_final: 0.7063 (p0) REVERT: D 94 ASN cc_start: 0.7752 (m110) cc_final: 0.7390 (m110) REVERT: D 105 MET cc_start: 0.8589 (mmt) cc_final: 0.8281 (mmt) REVERT: D 117 MET cc_start: 0.7435 (tpp) cc_final: 0.7220 (tpt) REVERT: D 163 ASP cc_start: 0.7107 (t0) cc_final: 0.6705 (t0) REVERT: D 171 MET cc_start: 0.7405 (mtm) cc_final: 0.7127 (mtt) REVERT: D 262 GLU cc_start: 0.7912 (tt0) cc_final: 0.7330 (pt0) REVERT: D 398 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6364 (tp30) REVERT: D 407 ASP cc_start: 0.7322 (t0) cc_final: 0.6947 (t0) REVERT: E 44 ASN cc_start: 0.7282 (t0) cc_final: 0.6477 (t0) REVERT: E 48 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7756 (mt-10) REVERT: E 93 GLU cc_start: 0.7439 (tp30) cc_final: 0.7009 (tp30) REVERT: E 186 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8484 (mm) REVERT: E 225 ASN cc_start: 0.8313 (m-40) cc_final: 0.8093 (m110) REVERT: E 235 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8023 (p) REVERT: E 266 LEU cc_start: 0.7406 (tp) cc_final: 0.7004 (tp) REVERT: E 271 GLN cc_start: 0.7641 (tt0) cc_final: 0.7264 (mt0) REVERT: E 469 THR cc_start: 0.8281 (m) cc_final: 0.8045 (p) REVERT: E 474 GLN cc_start: 0.7362 (pt0) cc_final: 0.7076 (mt0) outliers start: 61 outliers final: 23 residues processed: 263 average time/residue: 0.9366 time to fit residues: 284.8606 Evaluate side-chains 223 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN D 14 ASN D 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17471 Z= 0.230 Angle : 0.567 12.487 23782 Z= 0.271 Chirality : 0.044 0.222 2843 Planarity : 0.004 0.045 2856 Dihedral : 17.502 138.532 3207 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.74 % Allowed : 12.91 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1976 helix: 1.98 (0.19), residues: 754 sheet: -0.65 (0.25), residues: 398 loop : -0.90 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 187 HIS 0.004 0.001 HIS A 204 PHE 0.017 0.001 PHE A 256 TYR 0.010 0.001 TYR B 223 ARG 0.006 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 200 time to evaluate : 1.954 Fit side-chains revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7800 (pt0) cc_final: 0.7595 (pt0) REVERT: A 262 GLU cc_start: 0.7592 (tt0) cc_final: 0.7333 (tt0) REVERT: A 324 MET cc_start: 0.8101 (mtm) cc_final: 0.7673 (mtm) REVERT: A 407 ASP cc_start: 0.7256 (m-30) cc_final: 0.6889 (m-30) REVERT: B 57 ASN cc_start: 0.7831 (t0) cc_final: 0.6978 (m110) REVERT: B 93 MET cc_start: 0.8214 (mmm) cc_final: 0.7819 (mmt) REVERT: B 167 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6250 (pm20) REVERT: B 168 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.7012 (mmt180) REVERT: B 177 LYS cc_start: 0.8055 (tmtt) cc_final: 0.7845 (tmtp) REVERT: B 249 MET cc_start: 0.7422 (mmm) cc_final: 0.7091 (mmm) REVERT: B 268 ASP cc_start: 0.7931 (m-30) cc_final: 0.7416 (m-30) REVERT: B 275 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8123 (mt) REVERT: B 285 MET cc_start: 0.7646 (mmt) cc_final: 0.7280 (mmt) REVERT: B 314 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7310 (ttp) REVERT: C 5 GLU cc_start: 0.7224 (pt0) cc_final: 0.6754 (tt0) REVERT: C 46 LYS cc_start: 0.7319 (tttp) cc_final: 0.6826 (ttpt) REVERT: C 49 ASP cc_start: 0.7760 (m-30) cc_final: 0.7541 (m-30) REVERT: C 186 GLU cc_start: 0.7785 (tt0) cc_final: 0.7559 (tp30) REVERT: C 280 GLU cc_start: 0.7670 (mp0) cc_final: 0.7091 (mt-10) REVERT: C 489 ASP cc_start: 0.7869 (t70) cc_final: 0.7579 (t0) REVERT: D 13 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: D 89 ASP cc_start: 0.7288 (m-30) cc_final: 0.7067 (p0) REVERT: D 94 ASN cc_start: 0.7786 (m110) cc_final: 0.7489 (m110) REVERT: D 105 MET cc_start: 0.8587 (mmt) cc_final: 0.8294 (mmt) REVERT: D 108 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8051 (pp) REVERT: D 117 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7077 (tpt) REVERT: D 163 ASP cc_start: 0.7148 (t0) cc_final: 0.6709 (t0) REVERT: D 171 MET cc_start: 0.7434 (mtm) cc_final: 0.7125 (mtt) REVERT: D 398 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6599 (tp30) REVERT: D 407 ASP cc_start: 0.7323 (t0) cc_final: 0.6936 (t0) REVERT: E 186 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8502 (mm) REVERT: E 225 ASN cc_start: 0.8390 (m-40) cc_final: 0.8161 (m110) REVERT: E 235 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8207 (p) REVERT: E 266 LEU cc_start: 0.7404 (tp) cc_final: 0.6996 (tp) REVERT: E 271 GLN cc_start: 0.7666 (tt0) cc_final: 0.7433 (mt0) REVERT: E 469 THR cc_start: 0.8313 (m) cc_final: 0.8066 (p) REVERT: E 474 GLN cc_start: 0.7415 (pt0) cc_final: 0.7131 (mt0) outliers start: 69 outliers final: 30 residues processed: 245 average time/residue: 1.0001 time to fit residues: 285.7800 Evaluate side-chains 234 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS C 156 ASN D 14 ASN D 36 GLN D 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17471 Z= 0.198 Angle : 0.545 10.657 23782 Z= 0.259 Chirality : 0.044 0.263 2843 Planarity : 0.003 0.039 2856 Dihedral : 15.978 136.728 3207 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.18 % Allowed : 13.50 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1976 helix: 2.13 (0.19), residues: 753 sheet: -0.62 (0.25), residues: 395 loop : -0.88 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 187 HIS 0.004 0.001 HIS D 204 PHE 0.011 0.001 PHE A 256 TYR 0.009 0.001 TYR C 117 ARG 0.003 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 205 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7292 (p0) REVERT: A 36 GLN cc_start: 0.7712 (pt0) cc_final: 0.7452 (pt0) REVERT: A 200 ASP cc_start: 0.7783 (p0) cc_final: 0.7494 (p0) REVERT: A 258 LEU cc_start: 0.7071 (mt) cc_final: 0.6865 (mp) REVERT: A 262 GLU cc_start: 0.7593 (tt0) cc_final: 0.7338 (tt0) REVERT: A 324 MET cc_start: 0.8073 (mtm) cc_final: 0.7677 (mtm) REVERT: A 407 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: B 57 ASN cc_start: 0.7775 (t0) cc_final: 0.6968 (m110) REVERT: B 93 MET cc_start: 0.8180 (mmm) cc_final: 0.7919 (mmt) REVERT: B 167 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6252 (pm20) REVERT: B 168 ARG cc_start: 0.7712 (tpp-160) cc_final: 0.7010 (mmt180) REVERT: B 177 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7819 (tmtp) REVERT: B 182 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: B 249 MET cc_start: 0.7579 (mmm) cc_final: 0.7320 (mmm) REVERT: B 268 ASP cc_start: 0.7894 (m-30) cc_final: 0.7358 (m-30) REVERT: B 275 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8107 (mt) REVERT: B 285 MET cc_start: 0.7709 (mmt) cc_final: 0.7341 (mmt) REVERT: B 314 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7271 (ttp) REVERT: C 5 GLU cc_start: 0.7122 (pt0) cc_final: 0.6646 (tt0) REVERT: C 46 LYS cc_start: 0.7245 (tttp) cc_final: 0.6730 (ttpt) REVERT: C 49 ASP cc_start: 0.7726 (m-30) cc_final: 0.7501 (m-30) REVERT: C 186 GLU cc_start: 0.7772 (tt0) cc_final: 0.7556 (tp30) REVERT: C 280 GLU cc_start: 0.7636 (mp0) cc_final: 0.7046 (mt-10) REVERT: C 489 ASP cc_start: 0.7767 (t70) cc_final: 0.7482 (t0) REVERT: D 13 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: D 94 ASN cc_start: 0.7723 (m110) cc_final: 0.7403 (m110) REVERT: D 105 MET cc_start: 0.8550 (mmt) cc_final: 0.8269 (mmt) REVERT: D 108 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8070 (pp) REVERT: D 117 MET cc_start: 0.7321 (tpp) cc_final: 0.7062 (tpt) REVERT: D 163 ASP cc_start: 0.7212 (t0) cc_final: 0.6742 (t0) REVERT: D 171 MET cc_start: 0.7423 (mtm) cc_final: 0.7118 (mtt) REVERT: D 262 GLU cc_start: 0.7792 (tt0) cc_final: 0.7338 (pt0) REVERT: D 398 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6586 (tp30) REVERT: D 407 ASP cc_start: 0.7538 (t0) cc_final: 0.7130 (t0) REVERT: E 225 ASN cc_start: 0.8369 (m-40) cc_final: 0.8155 (m110) REVERT: E 235 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8168 (p) REVERT: E 266 LEU cc_start: 0.7463 (tp) cc_final: 0.7046 (tp) REVERT: E 469 THR cc_start: 0.8336 (m) cc_final: 0.8081 (p) REVERT: E 474 GLN cc_start: 0.7461 (pt0) cc_final: 0.7198 (mt0) outliers start: 77 outliers final: 32 residues processed: 255 average time/residue: 0.9354 time to fit residues: 276.5030 Evaluate side-chains 233 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 454 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 48 optimal weight: 0.0040 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 58 GLN C 156 ASN D 36 GLN D 58 GLN E 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17471 Z= 0.280 Angle : 0.589 11.215 23782 Z= 0.281 Chirality : 0.045 0.256 2843 Planarity : 0.004 0.039 2856 Dihedral : 15.213 132.593 3207 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.66 % Allowed : 14.48 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1976 helix: 1.99 (0.19), residues: 753 sheet: -0.60 (0.25), residues: 406 loop : -0.85 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 187 HIS 0.005 0.001 HIS A 104 PHE 0.016 0.001 PHE C 473 TYR 0.012 0.002 TYR E 117 ARG 0.006 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 197 time to evaluate : 2.041 Fit side-chains REVERT: A 30 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7315 (p0) REVERT: A 36 GLN cc_start: 0.7810 (pt0) cc_final: 0.7532 (pt0) REVERT: A 171 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7211 (ttt) REVERT: A 200 ASP cc_start: 0.7846 (p0) cc_final: 0.7478 (p0) REVERT: A 262 GLU cc_start: 0.7600 (tt0) cc_final: 0.7348 (tt0) REVERT: A 407 ASP cc_start: 0.7104 (m-30) cc_final: 0.6715 (m-30) REVERT: B 57 ASN cc_start: 0.7816 (t0) cc_final: 0.6970 (m110) REVERT: B 93 MET cc_start: 0.8161 (mmm) cc_final: 0.7820 (mmt) REVERT: B 167 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5923 (tp30) REVERT: B 168 ARG cc_start: 0.7657 (tpp-160) cc_final: 0.6634 (mmt180) REVERT: B 177 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7861 (tmtp) REVERT: B 249 MET cc_start: 0.7725 (mmm) cc_final: 0.7494 (mmm) REVERT: B 268 ASP cc_start: 0.7884 (m-30) cc_final: 0.7341 (m-30) REVERT: B 275 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8121 (mt) REVERT: B 314 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7119 (ttp) REVERT: B 424 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5248 (mm) REVERT: C 5 GLU cc_start: 0.7217 (pt0) cc_final: 0.6756 (tt0) REVERT: C 46 LYS cc_start: 0.7277 (tttp) cc_final: 0.6942 (mtpp) REVERT: C 280 GLU cc_start: 0.7806 (mp0) cc_final: 0.7163 (mt-10) REVERT: C 489 ASP cc_start: 0.7887 (t70) cc_final: 0.7580 (t0) REVERT: D 13 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: D 94 ASN cc_start: 0.7866 (m110) cc_final: 0.7552 (m110) REVERT: D 105 MET cc_start: 0.8520 (mmt) cc_final: 0.8251 (mmt) REVERT: D 108 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8054 (pp) REVERT: D 117 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6987 (tpt) REVERT: D 163 ASP cc_start: 0.7165 (t0) cc_final: 0.6694 (t0) REVERT: D 171 MET cc_start: 0.7547 (mtm) cc_final: 0.7233 (mtt) REVERT: D 262 GLU cc_start: 0.7770 (tt0) cc_final: 0.7305 (pt0) REVERT: D 324 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.3822 (mmm) REVERT: D 398 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6606 (tp30) REVERT: D 407 ASP cc_start: 0.7521 (t0) cc_final: 0.7150 (t0) REVERT: E 200 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7853 (p) REVERT: E 214 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7830 (mm) REVERT: E 225 ASN cc_start: 0.8450 (m-40) cc_final: 0.8216 (m110) REVERT: E 235 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8243 (p) REVERT: E 250 GLN cc_start: 0.8239 (mt0) cc_final: 0.7917 (mt0) REVERT: E 266 LEU cc_start: 0.7463 (tp) cc_final: 0.7110 (tp) REVERT: E 469 THR cc_start: 0.8431 (m) cc_final: 0.8153 (p) REVERT: E 474 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7164 (mt0) outliers start: 86 outliers final: 41 residues processed: 256 average time/residue: 0.9674 time to fit residues: 285.6497 Evaluate side-chains 249 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 194 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 112 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 15 optimal weight: 0.0060 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS D 14 ASN D 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17471 Z= 0.160 Angle : 0.543 10.372 23782 Z= 0.256 Chirality : 0.043 0.268 2843 Planarity : 0.003 0.041 2856 Dihedral : 14.403 130.745 3207 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.74 % Allowed : 15.67 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1976 helix: 2.15 (0.19), residues: 754 sheet: -0.61 (0.25), residues: 395 loop : -0.84 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 187 HIS 0.004 0.001 HIS D 204 PHE 0.011 0.001 PHE A 326 TYR 0.009 0.001 TYR A 277 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 202 time to evaluate : 1.937 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7262 (p0) REVERT: A 36 GLN cc_start: 0.7668 (pt0) cc_final: 0.7421 (pt0) REVERT: A 200 ASP cc_start: 0.7743 (p0) cc_final: 0.7447 (p0) REVERT: A 262 GLU cc_start: 0.7523 (tt0) cc_final: 0.7215 (tt0) REVERT: A 407 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6756 (m-30) REVERT: B 57 ASN cc_start: 0.7775 (t0) cc_final: 0.6955 (m110) REVERT: B 93 MET cc_start: 0.8102 (mmm) cc_final: 0.7784 (mmt) REVERT: B 167 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5912 (tp30) REVERT: B 168 ARG cc_start: 0.7666 (tpp-160) cc_final: 0.6655 (mmt180) REVERT: B 177 LYS cc_start: 0.8069 (tmtt) cc_final: 0.7829 (tmtp) REVERT: B 182 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: B 249 MET cc_start: 0.7549 (mmm) cc_final: 0.7297 (mmm) REVERT: B 268 ASP cc_start: 0.7845 (m-30) cc_final: 0.7233 (m-30) REVERT: B 275 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 424 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5292 (mm) REVERT: C 5 GLU cc_start: 0.7123 (pt0) cc_final: 0.6631 (tt0) REVERT: C 46 LYS cc_start: 0.7240 (tttp) cc_final: 0.6842 (mtpp) REVERT: D 13 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: D 105 MET cc_start: 0.8444 (mmt) cc_final: 0.8182 (mmt) REVERT: D 108 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8069 (pp) REVERT: D 117 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7031 (tpt) REVERT: D 163 ASP cc_start: 0.7162 (t0) cc_final: 0.6708 (t0) REVERT: D 171 MET cc_start: 0.7346 (mtm) cc_final: 0.7108 (mtt) REVERT: D 262 GLU cc_start: 0.7746 (tt0) cc_final: 0.7294 (pt0) REVERT: D 324 MET cc_start: 0.4757 (OUTLIER) cc_final: 0.3737 (mmm) REVERT: D 398 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6585 (tp30) REVERT: D 407 ASP cc_start: 0.7497 (t0) cc_final: 0.7100 (t0) REVERT: E 186 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8530 (mm) REVERT: E 200 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7841 (p) REVERT: E 225 ASN cc_start: 0.8383 (m-40) cc_final: 0.8178 (m110) REVERT: E 266 LEU cc_start: 0.7369 (tp) cc_final: 0.6989 (tp) REVERT: E 469 THR cc_start: 0.8430 (m) cc_final: 0.8169 (p) REVERT: E 474 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7183 (mt0) outliers start: 69 outliers final: 34 residues processed: 249 average time/residue: 0.9390 time to fit residues: 271.1647 Evaluate side-chains 240 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 193 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN D 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17471 Z= 0.233 Angle : 0.565 10.528 23782 Z= 0.268 Chirality : 0.044 0.249 2843 Planarity : 0.003 0.040 2856 Dihedral : 13.968 126.539 3207 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.39 % Allowed : 15.40 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 1976 helix: 2.07 (0.19), residues: 755 sheet: -0.57 (0.25), residues: 398 loop : -0.86 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 187 HIS 0.004 0.001 HIS A 204 PHE 0.014 0.001 PHE A 256 TYR 0.010 0.001 TYR E 117 ARG 0.004 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 198 time to evaluate : 1.907 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7269 (p0) REVERT: A 36 GLN cc_start: 0.7730 (pt0) cc_final: 0.7445 (pt0) REVERT: A 171 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7218 (ttt) REVERT: A 262 GLU cc_start: 0.7536 (tt0) cc_final: 0.7223 (tt0) REVERT: A 407 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: B 57 ASN cc_start: 0.7794 (t0) cc_final: 0.6976 (m110) REVERT: B 93 MET cc_start: 0.8203 (mmm) cc_final: 0.7890 (mmt) REVERT: B 167 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.5973 (tp30) REVERT: B 168 ARG cc_start: 0.7653 (tpp-160) cc_final: 0.6652 (mmt180) REVERT: B 177 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7849 (tmtp) REVERT: B 182 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: B 249 MET cc_start: 0.7528 (mmm) cc_final: 0.7254 (mmm) REVERT: B 268 ASP cc_start: 0.7809 (m-30) cc_final: 0.7171 (m-30) REVERT: B 284 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7487 (mt) REVERT: B 424 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5294 (mm) REVERT: C 5 GLU cc_start: 0.7200 (pt0) cc_final: 0.6745 (tt0) REVERT: C 46 LYS cc_start: 0.7249 (tttp) cc_final: 0.6814 (mtpp) REVERT: C 280 GLU cc_start: 0.7601 (mp0) cc_final: 0.7227 (mp0) REVERT: C 489 ASP cc_start: 0.7746 (t70) cc_final: 0.7478 (t0) REVERT: D 13 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: D 94 ASN cc_start: 0.7738 (m110) cc_final: 0.7453 (m110) REVERT: D 105 MET cc_start: 0.8479 (mmt) cc_final: 0.8224 (mmt) REVERT: D 108 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8076 (pp) REVERT: D 117 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.7020 (tpt) REVERT: D 163 ASP cc_start: 0.7080 (t0) cc_final: 0.6667 (t0) REVERT: D 171 MET cc_start: 0.7479 (mtm) cc_final: 0.7191 (mtt) REVERT: D 262 GLU cc_start: 0.7785 (tt0) cc_final: 0.7327 (pt0) REVERT: D 324 MET cc_start: 0.4778 (OUTLIER) cc_final: 0.3748 (mmm) REVERT: D 398 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6610 (tp30) REVERT: D 407 ASP cc_start: 0.7685 (t0) cc_final: 0.7212 (t0) REVERT: E 186 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8550 (mm) REVERT: E 200 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7916 (p) REVERT: E 225 ASN cc_start: 0.8419 (m-40) cc_final: 0.8211 (m110) REVERT: E 235 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8160 (p) REVERT: E 266 LEU cc_start: 0.7390 (tp) cc_final: 0.7032 (tp) REVERT: E 469 THR cc_start: 0.8449 (m) cc_final: 0.8180 (p) REVERT: E 474 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7170 (mt0) outliers start: 81 outliers final: 42 residues processed: 252 average time/residue: 0.9242 time to fit residues: 269.1988 Evaluate side-chains 247 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 190 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.0170 chunk 76 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN D 58 GLN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17471 Z= 0.176 Angle : 0.548 10.280 23782 Z= 0.257 Chirality : 0.044 0.243 2843 Planarity : 0.003 0.041 2856 Dihedral : 13.209 122.238 3204 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.96 % Allowed : 15.73 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1976 helix: 2.16 (0.19), residues: 756 sheet: -0.53 (0.25), residues: 395 loop : -0.84 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 187 HIS 0.004 0.001 HIS D 204 PHE 0.011 0.001 PHE A 256 TYR 0.010 0.001 TYR A 277 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 198 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7270 (p0) REVERT: A 262 GLU cc_start: 0.7514 (tt0) cc_final: 0.7273 (tt0) REVERT: A 407 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: B 57 ASN cc_start: 0.7739 (t0) cc_final: 0.6943 (m110) REVERT: B 167 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5994 (tp30) REVERT: B 177 LYS cc_start: 0.8067 (tmtt) cc_final: 0.7833 (tmtp) REVERT: B 182 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: B 249 MET cc_start: 0.7488 (mmm) cc_final: 0.7246 (mmm) REVERT: B 268 ASP cc_start: 0.7843 (m-30) cc_final: 0.7235 (m-30) REVERT: B 284 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7471 (mt) REVERT: B 314 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7001 (ttp) REVERT: B 424 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5292 (mm) REVERT: C 5 GLU cc_start: 0.7123 (pt0) cc_final: 0.6631 (tt0) REVERT: C 46 LYS cc_start: 0.7236 (tttp) cc_final: 0.6805 (mtpp) REVERT: D 13 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: D 57 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7655 (mtm110) REVERT: D 94 ASN cc_start: 0.7683 (m110) cc_final: 0.7423 (m110) REVERT: D 105 MET cc_start: 0.8407 (mmt) cc_final: 0.8166 (mmt) REVERT: D 108 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8071 (pp) REVERT: D 163 ASP cc_start: 0.7074 (t0) cc_final: 0.6669 (t0) REVERT: D 171 MET cc_start: 0.7342 (mtm) cc_final: 0.7118 (mtt) REVERT: D 262 GLU cc_start: 0.7790 (tt0) cc_final: 0.7378 (pt0) REVERT: D 324 MET cc_start: 0.4757 (OUTLIER) cc_final: 0.3693 (mmm) REVERT: D 398 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6590 (tp30) REVERT: D 407 ASP cc_start: 0.7514 (t0) cc_final: 0.7024 (t0) REVERT: E 186 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8532 (mm) REVERT: E 200 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7896 (p) REVERT: E 235 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8212 (p) REVERT: E 266 LEU cc_start: 0.7351 (tp) cc_final: 0.6973 (tp) REVERT: E 469 THR cc_start: 0.8430 (m) cc_final: 0.8179 (p) REVERT: E 474 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7175 (mt0) outliers start: 73 outliers final: 40 residues processed: 251 average time/residue: 0.9477 time to fit residues: 274.9139 Evaluate side-chains 245 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 191 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 139 optimal weight: 0.0670 chunk 54 optimal weight: 6.9990 chunk 160 optimal weight: 0.5980 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 36 GLN D 58 GLN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17471 Z= 0.156 Angle : 0.533 10.058 23782 Z= 0.252 Chirality : 0.043 0.266 2843 Planarity : 0.003 0.041 2856 Dihedral : 12.525 114.968 3204 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.15 % Allowed : 16.87 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1976 helix: 2.18 (0.19), residues: 764 sheet: -0.48 (0.25), residues: 396 loop : -0.83 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 187 HIS 0.004 0.001 HIS D 204 PHE 0.016 0.001 PHE D 227 TYR 0.009 0.001 TYR A 277 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 207 time to evaluate : 2.154 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7222 (p0) REVERT: A 262 GLU cc_start: 0.7515 (tt0) cc_final: 0.7279 (tt0) REVERT: A 407 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6727 (m-30) REVERT: B 57 ASN cc_start: 0.7648 (t0) cc_final: 0.6949 (m110) REVERT: B 167 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6403 (pm20) REVERT: B 177 LYS cc_start: 0.8036 (tmtt) cc_final: 0.7810 (tmtp) REVERT: B 182 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: B 268 ASP cc_start: 0.7871 (m-30) cc_final: 0.7241 (m-30) REVERT: B 284 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7468 (mt) REVERT: B 424 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5319 (mm) REVERT: C 5 GLU cc_start: 0.7112 (pt0) cc_final: 0.6616 (tt0) REVERT: C 46 LYS cc_start: 0.7236 (tttp) cc_final: 0.6783 (mtpp) REVERT: C 125 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8919 (mp) REVERT: C 168 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6412 (t0) REVERT: D 13 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: D 57 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7653 (mtm110) REVERT: D 105 MET cc_start: 0.8452 (mmt) cc_final: 0.8188 (mmt) REVERT: D 108 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8018 (pp) REVERT: D 163 ASP cc_start: 0.7070 (t0) cc_final: 0.6686 (t0) REVERT: D 171 MET cc_start: 0.7317 (mtm) cc_final: 0.7098 (mtt) REVERT: D 262 GLU cc_start: 0.7803 (tt0) cc_final: 0.7365 (pt0) REVERT: D 407 ASP cc_start: 0.7525 (t0) cc_final: 0.7015 (t0) REVERT: E 186 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8509 (mm) REVERT: E 200 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7865 (p) REVERT: E 225 ASN cc_start: 0.8289 (m110) cc_final: 0.7675 (m-40) REVERT: E 235 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8206 (p) REVERT: E 266 LEU cc_start: 0.7292 (tp) cc_final: 0.6993 (tp) REVERT: E 469 THR cc_start: 0.8408 (m) cc_final: 0.8170 (p) REVERT: E 474 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7146 (mt0) outliers start: 58 outliers final: 35 residues processed: 247 average time/residue: 0.8931 time to fit residues: 257.6762 Evaluate side-chains 242 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 197 optimal weight: 0.0980 chunk 181 optimal weight: 0.0870 chunk 157 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 96 optimal weight: 0.0010 chunk 124 optimal weight: 0.9980 overall best weight: 0.8366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 58 GLN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17471 Z= 0.173 Angle : 0.541 10.022 23782 Z= 0.256 Chirality : 0.043 0.268 2843 Planarity : 0.003 0.040 2856 Dihedral : 12.288 110.767 3204 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.82 % Allowed : 17.30 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1976 helix: 2.15 (0.19), residues: 765 sheet: -0.42 (0.25), residues: 396 loop : -0.84 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 187 HIS 0.004 0.001 HIS D 204 PHE 0.019 0.001 PHE D 284 TYR 0.010 0.001 TYR A 277 ARG 0.002 0.000 ARG C 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7213 (p0) REVERT: A 262 GLU cc_start: 0.7502 (tt0) cc_final: 0.7264 (tt0) REVERT: A 407 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: B 57 ASN cc_start: 0.7651 (t0) cc_final: 0.6966 (m110) REVERT: B 167 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: B 177 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7807 (tmtp) REVERT: B 182 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: B 268 ASP cc_start: 0.7873 (m-30) cc_final: 0.7228 (m-30) REVERT: B 284 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7466 (mt) REVERT: B 424 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5317 (mm) REVERT: C 5 GLU cc_start: 0.7119 (pt0) cc_final: 0.6624 (tt0) REVERT: C 46 LYS cc_start: 0.7230 (tttp) cc_final: 0.6780 (mtpp) REVERT: C 125 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8920 (mp) REVERT: C 168 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6350 (t0) REVERT: D 13 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7491 (pm20) REVERT: D 57 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7540 (mtm110) REVERT: D 105 MET cc_start: 0.8451 (mmt) cc_final: 0.8205 (mmt) REVERT: D 108 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8042 (pp) REVERT: D 163 ASP cc_start: 0.7073 (t0) cc_final: 0.6679 (t0) REVERT: D 171 MET cc_start: 0.7327 (mtm) cc_final: 0.7104 (mtt) REVERT: D 262 GLU cc_start: 0.7817 (tt0) cc_final: 0.7377 (pt0) REVERT: D 398 GLU cc_start: 0.6998 (tp30) cc_final: 0.6248 (tp30) REVERT: D 407 ASP cc_start: 0.7524 (t0) cc_final: 0.7020 (t0) REVERT: E 186 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8536 (mm) REVERT: E 200 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7874 (p) REVERT: E 225 ASN cc_start: 0.8245 (m110) cc_final: 0.7628 (m-40) REVERT: E 235 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8201 (p) REVERT: E 266 LEU cc_start: 0.7406 (tp) cc_final: 0.7028 (tp) REVERT: E 469 THR cc_start: 0.8418 (m) cc_final: 0.8176 (p) REVERT: E 474 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7171 (mt0) outliers start: 52 outliers final: 34 residues processed: 237 average time/residue: 0.9544 time to fit residues: 260.8196 Evaluate side-chains 241 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 193 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN D 36 GLN D 58 GLN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107951 restraints weight = 22638.884| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.19 r_work: 0.3118 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17471 Z= 0.160 Angle : 0.529 11.588 23782 Z= 0.251 Chirality : 0.043 0.262 2843 Planarity : 0.003 0.041 2856 Dihedral : 11.593 97.048 3204 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.82 % Allowed : 17.41 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1976 helix: 2.24 (0.19), residues: 762 sheet: -0.41 (0.25), residues: 396 loop : -0.82 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 187 HIS 0.004 0.001 HIS D 204 PHE 0.018 0.001 PHE D 284 TYR 0.010 0.001 TYR A 277 ARG 0.002 0.000 ARG E 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5403.24 seconds wall clock time: 96 minutes 45.47 seconds (5805.47 seconds total)