Starting phenix.real_space_refine on Mon Jun 16 01:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqn_39500/06_2025/8yqn_39500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqn_39500/06_2025/8yqn_39500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yqn_39500/06_2025/8yqn_39500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqn_39500/06_2025/8yqn_39500.map" model { file = "/net/cci-nas-00/data/ceres_data/8yqn_39500/06_2025/8yqn_39500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqn_39500/06_2025/8yqn_39500.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 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 4 5.49 5 S 102 5.16 5 C 11733 2.51 5 N 2846 2.21 5 O 3371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18056 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3218 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Chain: "B" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3462 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 398} Chain breaks: 1 Chain: "C" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3308 Classifications: {'peptide': 408} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 383} Chain breaks: 1 Chain: "D" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3218 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Chain: "E" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3355 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 1 Chain: "F" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 473 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "G" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 473 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 3} 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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'NAG': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 11.70, per 1000 atoms: 0.65 Number of scatterers: 18056 At special positions: 0 Unit cell: (100.7, 133, 169.1, 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 102 16.00 P 4 15.00 O 3371 8.00 N 2846 7.00 C 11733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.06 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 416 " - pdb=" SG CYS E 420 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 24 " distance=2.03 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 41 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 54 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 60 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 24 " distance=2.03 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 41 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 54 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 60 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-2 " MAN H 5 " - " MAN H 6 " " MAN H 8 " - " MAN H 9 " " MAN I 5 " - " MAN I 6 " " MAN I 8 " - " MAN I 9 " ALPHA1-3 " BMA H 3 " - " MAN H 8 " " MAN H 4 " - " MAN H 7 " " BMA I 3 " - " MAN I 8 " " MAN I 4 " - " MAN I 7 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " NAG L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " BETA1-4 " 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 " - " NAG L 3 " NAG-ASN " NAG B 601 " - " ASN B 70 " " NAG B 602 " - " ASN B 208 " " NAG E 501 " - " ASN E 68 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN B 143 " " NAG K 1 " - " ASN C 141 " " NAG L 1 " - " ASN E 141 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4170 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 24 sheets defined 40.9% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.010A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.634A pdb=" N ASP A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 85' Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.895A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.644A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.930A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.654A pdb=" N ILE A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 374 through 434 removed outlier: 3.582A pdb=" N TRP A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.587A pdb=" N LEU B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.564A pdb=" N SER B 253 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 254' Processing helix chain 'B' and resid 255 through 275 removed outlier: 3.661A pdb=" N ALA B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 417 through 478 removed outlier: 3.623A pdb=" N ASN B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.969A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.691A pdb=" N VAL C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 4.026A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 238 removed outlier: 5.084A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.555A pdb=" N GLY C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 324 removed outlier: 3.740A pdb=" N ARG C 319 " --> pdb=" O PRO C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 4.170A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 removed outlier: 3.728A pdb=" N LYS C 409 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.128A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.583A pdb=" N ASP D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL D 85 " --> pdb=" O SER D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 85' Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 218 through 232 removed outlier: 3.626A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 241 through 264 removed outlier: 3.776A pdb=" N LEU D 258 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 319 removed outlier: 3.535A pdb=" N THR D 319 " --> pdb=" O ILE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 370 through 433 removed outlier: 4.017A pdb=" N MET D 386 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL D 425 " --> pdb=" O GLY D 421 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARG D 429 " --> pdb=" O VAL D 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.859A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 220 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.811A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.592A pdb=" N PHE E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 415 through 473 removed outlier: 4.557A pdb=" N ASN E 421 " --> pdb=" O VAL E 417 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN E 437 " --> pdb=" O SER E 433 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.156A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.156A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN A 36 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ILE A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N THR A 32 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.827A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.775A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 94 removed outlier: 6.793A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.913A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.913A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR C 51 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE C 55 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 37 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN C 57 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU C 35 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA C 59 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL C 33 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N THR C 61 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL C 31 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.586A pdb=" N CYS C 142 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.586A pdb=" N CYS C 142 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR C 204 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG C 198 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.180A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.180A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN D 53 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU D 40 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ARG D 55 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE D 38 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ARG D 57 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLN D 36 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN D 59 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY D 34 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ILE D 61 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N THR D 32 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.787A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.025A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.025A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.382A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.382A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 Processing sheet with id=AC3, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 41 removed outlier: 3.633A pdb=" N GLY F 40 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AC6, first strand: chain 'G' and resid 35 through 40 removed outlier: 3.705A pdb=" N GLY G 40 " --> pdb=" O TYR G 25 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2700 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: 6.34 Time building geometry restraints manager: 6.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3091 1.32 - 1.45: 4930 1.45 - 1.58: 10327 1.58 - 1.71: 8 1.71 - 1.84: 156 Bond restraints: 18512 Sorted by residual: bond pdb=" C ALA E 450 " pdb=" N CYS E 451 " ideal model delta sigma weight residual 1.335 1.556 -0.221 1.35e-02 5.49e+03 2.68e+02 bond pdb=" C TYR D 203 " pdb=" O TYR D 203 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.18e-02 7.18e+03 1.20e+01 bond pdb=" C ARG C 20 " pdb=" N PRO C 21 " ideal model delta sigma weight residual 1.334 1.414 -0.081 2.34e-02 1.83e+03 1.18e+01 bond pdb=" CA PHE E 452 " pdb=" C PHE E 452 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.26e-02 6.30e+03 1.15e+01 bond pdb=" C ASP E 483 " pdb=" N PRO E 484 " ideal model delta sigma weight residual 1.331 1.358 -0.026 7.90e-03 1.60e+04 1.12e+01 ... (remaining 18507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 23896 1.92 - 3.84: 1153 3.84 - 5.75: 142 5.75 - 7.67: 20 7.67 - 9.59: 7 Bond angle restraints: 25218 Sorted by residual: angle pdb=" O ARG C 20 " pdb=" C ARG C 20 " pdb=" N PRO C 21 " ideal model delta sigma weight residual 121.28 111.94 9.34 1.00e+00 1.00e+00 8.73e+01 angle pdb=" CA ARG C 20 " pdb=" C ARG C 20 " pdb=" N PRO C 21 " ideal model delta sigma weight residual 118.85 127.28 -8.43 9.50e-01 1.11e+00 7.87e+01 angle pdb=" O ALA E 450 " pdb=" C ALA E 450 " pdb=" N CYS E 451 " ideal model delta sigma weight residual 122.07 129.34 -7.27 1.03e+00 9.43e-01 4.98e+01 angle pdb=" C ARG B 113 " pdb=" CA ARG B 113 " pdb=" CB ARG B 113 " ideal model delta sigma weight residual 108.91 118.50 -9.59 1.53e+00 4.27e-01 3.93e+01 angle pdb=" N PHE E 452 " pdb=" CA PHE E 452 " pdb=" C PHE E 452 " ideal model delta sigma weight residual 111.14 105.06 6.08 1.08e+00 8.57e-01 3.17e+01 ... (remaining 25213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.84: 10906 25.84 - 51.68: 424 51.68 - 77.52: 89 77.52 - 103.36: 33 103.36 - 129.20: 18 Dihedral angle restraints: 11470 sinusoidal: 5062 harmonic: 6408 Sorted by residual: dihedral pdb=" CB CYS F 3 " pdb=" SG CYS F 3 " pdb=" SG CYS F 24 " pdb=" CB CYS F 24 " ideal model delta sinusoidal sigma weight residual -86.00 -165.16 79.16 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CB CYS E 128 " pdb=" SG CYS E 128 " pdb=" SG CYS E 142 " pdb=" CB CYS E 142 " ideal model delta sinusoidal sigma weight residual 93.00 56.38 36.62 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" C37 POV C 501 " pdb=" C38 POV C 501 " pdb=" C39 POV C 501 " pdb="C310 POV C 501 " ideal model delta sinusoidal sigma weight residual -179.61 -50.41 -129.20 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 11467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2768 0.102 - 0.203: 213 0.203 - 0.305: 8 0.305 - 0.406: 0 0.406 - 0.508: 1 Chirality restraints: 2990 Sorted by residual: chirality pdb=" C1 MAN I 9 " pdb=" O2 MAN I 8 " pdb=" C2 MAN I 9 " pdb=" O5 MAN I 9 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.07e+02 chirality pdb=" C1 MAN I 8 " pdb=" O3 BMA I 3 " pdb=" C2 MAN I 8 " pdb=" O5 MAN I 8 " both_signs ideal model delta sigma weight residual False 2.40 2.48 -0.08 2.00e-02 2.50e+03 1.65e+01 chirality pdb=" C1 MAN H 9 " pdb=" O2 MAN H 8 " pdb=" C2 MAN H 9 " pdb=" O5 MAN H 9 " both_signs ideal model delta sigma weight residual False 2.40 2.48 -0.08 2.00e-02 2.50e+03 1.57e+01 ... (remaining 2987 not shown) Planarity restraints: 3088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.098 2.00e-02 2.50e+03 8.30e-02 8.62e+01 pdb=" C7 NAG I 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.134 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.096 2.00e-02 2.50e+03 8.17e-02 8.35e+01 pdb=" C7 NAG H 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.024 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.131 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.056 2.00e-02 2.50e+03 4.72e-02 2.78e+01 pdb=" C7 NAG K 2 " 0.001 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.080 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.014 2.00e-02 2.50e+03 ... (remaining 3085 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 126 2.63 - 3.20: 15556 3.20 - 3.76: 26890 3.76 - 4.33: 40022 4.33 - 4.90: 64276 Nonbonded interactions: 146870 Sorted by model distance: nonbonded pdb=" O PRO D 194 " pdb=" NE2 GLN G 10 " model vdw 2.060 3.120 nonbonded pdb=" O PRO A 194 " pdb=" NE2 GLN F 10 " model vdw 2.097 3.120 nonbonded pdb=" OH TYR D 190 " pdb=" OD2 ASP G 31 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR D 381 " pdb=" ND2 ASN E 431 " model vdw 2.230 3.120 nonbonded pdb=" OD2 ASP D 152 " pdb=" OG1 THR D 154 " model vdw 2.259 3.040 ... (remaining 146865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.850 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.120 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 0.221 18559 Z= 0.339 Angle : 0.924 15.233 25342 Z= 0.520 Chirality : 0.056 0.508 2990 Planarity : 0.010 0.125 3080 Dihedral : 15.811 129.195 7258 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.15 % Allowed : 0.70 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.16), residues: 2142 helix: -1.59 (0.16), residues: 766 sheet: -1.03 (0.21), residues: 485 loop : -2.12 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 67 HIS 0.013 0.002 HIS A 299 PHE 0.030 0.002 PHE E 422 TYR 0.032 0.002 TYR D 93 ARG 0.025 0.003 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00818 ( 8) link_NAG-ASN : angle 3.02028 ( 24) link_ALPHA1-6 : bond 0.00606 ( 6) link_ALPHA1-6 : angle 2.11451 ( 18) link_BETA1-4 : bond 0.00766 ( 10) link_BETA1-4 : angle 3.24183 ( 30) link_ALPHA1-2 : bond 0.02181 ( 4) link_ALPHA1-2 : angle 5.60388 ( 12) link_ALPHA1-3 : bond 0.01229 ( 4) link_ALPHA1-3 : angle 3.30992 ( 12) hydrogen bonds : bond 0.14625 ( 852) hydrogen bonds : angle 6.57080 ( 2700) SS BOND : bond 0.00916 ( 14) SS BOND : angle 2.20424 ( 28) covalent geometry : bond 0.00626 (18512) covalent geometry : angle 0.89919 (25218) Misc. bond : bond 0.00326 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 221 time to evaluate : 2.141 Fit side-chains REVERT: C 194 ARG cc_start: 0.8330 (ptm160) cc_final: 0.8044 (ptp-170) REVERT: E 449 LYS cc_start: 0.7354 (ttpt) cc_final: 0.7016 (tptt) REVERT: G 31 ASP cc_start: 0.8154 (p0) cc_final: 0.7940 (p0) outliers start: 3 outliers final: 1 residues processed: 224 average time/residue: 1.4385 time to fit residues: 359.0556 Evaluate side-chains 166 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 48 GLN A 186 HIS A 204 HIS B 28 ASN ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN B 101 GLN B 103 HIS B 267 GLN C 96 ASN C 140 GLN C 159 GLN C 183 ASN C 310 ASN D 186 HIS D 204 HIS D 394 ASN E 27 HIS E 140 GLN E 188 HIS E 271 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.085985 restraints weight = 21231.569| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.87 r_work: 0.2932 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 18559 Z= 0.213 Angle : 0.711 8.324 25342 Z= 0.366 Chirality : 0.049 0.203 2990 Planarity : 0.005 0.045 3080 Dihedral : 12.014 120.897 3067 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.70 % Allowed : 6.16 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.21 (0.17), residues: 2142 helix: 0.98 (0.18), residues: 783 sheet: -0.04 (0.23), residues: 465 loop : -1.16 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 67 HIS 0.009 0.002 HIS A 204 PHE 0.021 0.002 PHE A 284 TYR 0.026 0.002 TYR D 93 ARG 0.006 0.001 ARG B 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 8) link_NAG-ASN : angle 2.20215 ( 24) link_ALPHA1-6 : bond 0.00433 ( 6) link_ALPHA1-6 : angle 1.50159 ( 18) link_BETA1-4 : bond 0.00525 ( 10) link_BETA1-4 : angle 3.05713 ( 30) link_ALPHA1-2 : bond 0.00760 ( 4) link_ALPHA1-2 : angle 2.90574 ( 12) link_ALPHA1-3 : bond 0.01049 ( 4) link_ALPHA1-3 : angle 1.63169 ( 12) hydrogen bonds : bond 0.07322 ( 852) hydrogen bonds : angle 4.82525 ( 2700) SS BOND : bond 0.00469 ( 14) SS BOND : angle 1.38742 ( 28) covalent geometry : bond 0.00500 (18512) covalent geometry : angle 0.69563 (25218) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 2.364 Fit side-chains REVERT: A 329 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6677 (mmm) REVERT: C 13 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: C 413 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7562 (mt-10) REVERT: C 452 PHE cc_start: 0.7873 (m-80) cc_final: 0.7212 (t80) REVERT: D 77 LYS cc_start: 0.8815 (mttm) cc_final: 0.8574 (mtmt) REVERT: D 320 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6850 (mm) REVERT: D 397 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7426 (pt0) REVERT: E 33 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8106 (pt) REVERT: E 448 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7783 (t0) REVERT: E 449 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7267 (tptp) REVERT: E 485 ARG cc_start: 0.8383 (mtp85) cc_final: 0.8178 (mtm110) outliers start: 34 outliers final: 14 residues processed: 210 average time/residue: 1.9200 time to fit residues: 449.3069 Evaluate side-chains 190 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 14 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 83 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN C 95 ASN C 310 ASN D 408 HIS ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.086788 restraints weight = 21262.311| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.84 r_work: 0.2965 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18559 Z= 0.179 Angle : 0.643 9.845 25342 Z= 0.329 Chirality : 0.047 0.192 2990 Planarity : 0.005 0.045 3080 Dihedral : 10.533 114.567 3067 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 2.15 % Allowed : 7.11 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.65 (0.18), residues: 2142 helix: 1.87 (0.18), residues: 783 sheet: 0.45 (0.23), residues: 462 loop : -0.87 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 176 HIS 0.005 0.001 HIS D 104 PHE 0.018 0.002 PHE E 422 TYR 0.017 0.002 TYR D 93 ARG 0.004 0.001 ARG E 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 8) link_NAG-ASN : angle 2.11124 ( 24) link_ALPHA1-6 : bond 0.00463 ( 6) link_ALPHA1-6 : angle 1.48875 ( 18) link_BETA1-4 : bond 0.00511 ( 10) link_BETA1-4 : angle 2.94487 ( 30) link_ALPHA1-2 : bond 0.00971 ( 4) link_ALPHA1-2 : angle 2.59774 ( 12) link_ALPHA1-3 : bond 0.00857 ( 4) link_ALPHA1-3 : angle 1.39416 ( 12) hydrogen bonds : bond 0.06863 ( 852) hydrogen bonds : angle 4.61135 ( 2700) SS BOND : bond 0.00378 ( 14) SS BOND : angle 1.12919 ( 28) covalent geometry : bond 0.00416 (18512) covalent geometry : angle 0.62801 (25218) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 2.097 Fit side-chains REVERT: A 193 CYS cc_start: 0.8583 (m) cc_final: 0.7394 (p) REVERT: A 329 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6331 (mmm) REVERT: B 33 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8539 (mp) REVERT: B 92 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8416 (mt) REVERT: B 245 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8626 (mp) REVERT: C 13 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: C 452 PHE cc_start: 0.7946 (m-80) cc_final: 0.7298 (t80) REVERT: D 77 LYS cc_start: 0.8870 (mttm) cc_final: 0.8668 (mtmt) REVERT: D 308 MET cc_start: 0.8915 (tpp) cc_final: 0.8632 (tpp) REVERT: D 320 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6887 (mm) REVERT: D 397 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7450 (pt0) REVERT: E 33 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8121 (pt) REVERT: E 449 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7316 (tptp) REVERT: E 485 ARG cc_start: 0.8408 (mtp85) cc_final: 0.8206 (mtm110) outliers start: 43 outliers final: 16 residues processed: 211 average time/residue: 1.7252 time to fit residues: 412.9656 Evaluate side-chains 198 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain F residue 14 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 7 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 310 ASN E 99 GLN E 181 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087351 restraints weight = 21365.961| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.85 r_work: 0.2977 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18559 Z= 0.154 Angle : 0.595 6.619 25342 Z= 0.305 Chirality : 0.045 0.206 2990 Planarity : 0.005 0.045 3080 Dihedral : 9.770 109.317 3066 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.11 % Rotamer: Outliers : 2.15 % Allowed : 8.06 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.98 (0.18), residues: 2142 helix: 2.21 (0.18), residues: 783 sheet: 0.56 (0.23), residues: 484 loop : -0.75 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 187 HIS 0.005 0.001 HIS D 408 PHE 0.015 0.001 PHE B 473 TYR 0.013 0.002 TYR B 202 ARG 0.003 0.000 ARG D 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 8) link_NAG-ASN : angle 2.05449 ( 24) link_ALPHA1-6 : bond 0.00480 ( 6) link_ALPHA1-6 : angle 1.45967 ( 18) link_BETA1-4 : bond 0.00428 ( 10) link_BETA1-4 : angle 2.68855 ( 30) link_ALPHA1-2 : bond 0.01076 ( 4) link_ALPHA1-2 : angle 2.09260 ( 12) link_ALPHA1-3 : bond 0.00892 ( 4) link_ALPHA1-3 : angle 1.20684 ( 12) hydrogen bonds : bond 0.06356 ( 852) hydrogen bonds : angle 4.47126 ( 2700) SS BOND : bond 0.00340 ( 14) SS BOND : angle 0.94659 ( 28) covalent geometry : bond 0.00347 (18512) covalent geometry : angle 0.58074 (25218) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 2.221 Fit side-chains REVERT: A 193 CYS cc_start: 0.8559 (m) cc_final: 0.7325 (p) REVERT: A 329 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6289 (mmm) REVERT: B 33 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8501 (mp) REVERT: C 194 ARG cc_start: 0.8858 (ptm160) cc_final: 0.8285 (ptp-170) REVERT: C 452 PHE cc_start: 0.8054 (m-80) cc_final: 0.7421 (t80) REVERT: D 397 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7508 (pt0) REVERT: E 33 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8087 (pt) REVERT: E 449 LYS cc_start: 0.7766 (ttpt) cc_final: 0.7365 (tptp) outliers start: 43 outliers final: 18 residues processed: 212 average time/residue: 1.2702 time to fit residues: 304.7707 Evaluate side-chains 201 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 23 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 88 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN C 119 GLN C 310 ASN C 466 ASN E 300 ASN E 474 GLN G 10 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.085989 restraints weight = 21377.315| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.85 r_work: 0.2954 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18559 Z= 0.191 Angle : 0.635 6.675 25342 Z= 0.325 Chirality : 0.047 0.215 2990 Planarity : 0.005 0.047 3080 Dihedral : 9.827 107.450 3066 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 2.30 % Allowed : 8.46 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2142 helix: 2.23 (0.18), residues: 785 sheet: 0.57 (0.23), residues: 484 loop : -0.73 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 176 HIS 0.005 0.001 HIS B 60 PHE 0.017 0.002 PHE E 467 TYR 0.015 0.002 TYR B 202 ARG 0.004 0.001 ARG E 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 8) link_NAG-ASN : angle 2.11716 ( 24) link_ALPHA1-6 : bond 0.00444 ( 6) link_ALPHA1-6 : angle 1.51055 ( 18) link_BETA1-4 : bond 0.00431 ( 10) link_BETA1-4 : angle 2.82414 ( 30) link_ALPHA1-2 : bond 0.00877 ( 4) link_ALPHA1-2 : angle 2.25087 ( 12) link_ALPHA1-3 : bond 0.00812 ( 4) link_ALPHA1-3 : angle 1.33117 ( 12) hydrogen bonds : bond 0.06884 ( 852) hydrogen bonds : angle 4.57338 ( 2700) SS BOND : bond 0.00436 ( 14) SS BOND : angle 1.15297 ( 28) covalent geometry : bond 0.00449 (18512) covalent geometry : angle 0.62074 (25218) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 2.145 Fit side-chains REVERT: A 193 CYS cc_start: 0.8541 (m) cc_final: 0.7376 (p) REVERT: A 329 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6339 (mmm) REVERT: B 33 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 92 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8426 (mt) REVERT: C 13 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: C 194 ARG cc_start: 0.8904 (ptm160) cc_final: 0.8303 (ptp-170) REVERT: C 452 PHE cc_start: 0.7892 (m-80) cc_final: 0.7249 (t80) REVERT: D 320 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.6870 (mm) REVERT: D 397 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7453 (pt0) REVERT: E 33 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8127 (pt) REVERT: E 449 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7381 (ttmm) outliers start: 46 outliers final: 23 residues processed: 207 average time/residue: 1.1864 time to fit residues: 278.2792 Evaluate side-chains 199 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 329 MET Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 23 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 97 optimal weight: 0.0060 chunk 110 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 310 ASN E 271 GLN G 10 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.088827 restraints weight = 21350.209| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.85 r_work: 0.2998 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18559 Z= 0.123 Angle : 0.546 6.582 25342 Z= 0.280 Chirality : 0.043 0.176 2990 Planarity : 0.004 0.047 3080 Dihedral : 9.238 103.434 3066 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.25 % Rotamer: Outliers : 1.50 % Allowed : 9.66 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2142 helix: 2.53 (0.18), residues: 785 sheet: 0.71 (0.23), residues: 484 loop : -0.55 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 187 HIS 0.005 0.001 HIS D 408 PHE 0.011 0.001 PHE B 473 TYR 0.015 0.001 TYR G 25 ARG 0.002 0.000 ARG D 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 1.96588 ( 24) link_ALPHA1-6 : bond 0.00520 ( 6) link_ALPHA1-6 : angle 1.44554 ( 18) link_BETA1-4 : bond 0.00422 ( 10) link_BETA1-4 : angle 2.35786 ( 30) link_ALPHA1-2 : bond 0.00653 ( 4) link_ALPHA1-2 : angle 1.92433 ( 12) link_ALPHA1-3 : bond 0.00878 ( 4) link_ALPHA1-3 : angle 1.21683 ( 12) hydrogen bonds : bond 0.05709 ( 852) hydrogen bonds : angle 4.32201 ( 2700) SS BOND : bond 0.00285 ( 14) SS BOND : angle 0.77435 ( 28) covalent geometry : bond 0.00263 (18512) covalent geometry : angle 0.53352 (25218) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 1.924 Fit side-chains REVERT: A 193 CYS cc_start: 0.8474 (m) cc_final: 0.7211 (p) REVERT: A 386 MET cc_start: 0.8395 (mtp) cc_final: 0.8154 (mtm) REVERT: A 404 MET cc_start: 0.8425 (ttp) cc_final: 0.8194 (ttp) REVERT: B 33 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8473 (mp) REVERT: B 92 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8394 (mt) REVERT: C 13 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: C 194 ARG cc_start: 0.8799 (ptm160) cc_final: 0.8192 (ptp-170) REVERT: C 452 PHE cc_start: 0.8049 (m-80) cc_final: 0.7413 (t80) REVERT: D 191 THR cc_start: 0.8715 (m) cc_final: 0.8456 (p) REVERT: D 397 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7460 (pt0) REVERT: E 33 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8021 (pt) REVERT: E 198 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: E 449 LYS cc_start: 0.7715 (ttpt) cc_final: 0.7314 (ttmm) outliers start: 30 outliers final: 14 residues processed: 199 average time/residue: 1.2065 time to fit residues: 270.7215 Evaluate side-chains 197 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain F residue 14 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 160 optimal weight: 0.0040 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 310 ASN C 466 ASN G 10 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.090056 restraints weight = 21275.723| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.85 r_work: 0.3015 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18559 Z= 0.113 Angle : 0.530 6.477 25342 Z= 0.270 Chirality : 0.043 0.187 2990 Planarity : 0.004 0.047 3080 Dihedral : 8.847 100.590 3066 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 1.35 % Allowed : 10.41 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2142 helix: 2.68 (0.18), residues: 785 sheet: 0.78 (0.23), residues: 484 loop : -0.45 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 311 HIS 0.005 0.001 HIS B 60 PHE 0.012 0.001 PHE B 294 TYR 0.018 0.001 TYR F 25 ARG 0.002 0.000 ARG D 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 8) link_NAG-ASN : angle 1.89372 ( 24) link_ALPHA1-6 : bond 0.00557 ( 6) link_ALPHA1-6 : angle 1.46904 ( 18) link_BETA1-4 : bond 0.00419 ( 10) link_BETA1-4 : angle 2.20442 ( 30) link_ALPHA1-2 : bond 0.00526 ( 4) link_ALPHA1-2 : angle 1.91817 ( 12) link_ALPHA1-3 : bond 0.00868 ( 4) link_ALPHA1-3 : angle 1.27646 ( 12) hydrogen bonds : bond 0.05374 ( 852) hydrogen bonds : angle 4.19089 ( 2700) SS BOND : bond 0.00265 ( 14) SS BOND : angle 0.70152 ( 28) covalent geometry : bond 0.00236 (18512) covalent geometry : angle 0.51773 (25218) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 1.865 Fit side-chains REVERT: A 193 CYS cc_start: 0.8443 (m) cc_final: 0.7207 (p) REVERT: A 224 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8621 (tt) REVERT: A 324 MET cc_start: 0.4764 (tpt) cc_final: 0.4490 (tpp) REVERT: A 386 MET cc_start: 0.8370 (mtp) cc_final: 0.8137 (mtm) REVERT: B 33 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 92 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8361 (mp) REVERT: B 241 PHE cc_start: 0.8317 (m-10) cc_final: 0.6700 (t80) REVERT: C 13 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: C 194 ARG cc_start: 0.8769 (ptm160) cc_final: 0.8156 (ptp-170) REVERT: C 452 PHE cc_start: 0.8029 (m-80) cc_final: 0.7403 (t80) REVERT: D 115 LYS cc_start: 0.8356 (tmtt) cc_final: 0.8104 (mtpp) REVERT: D 191 THR cc_start: 0.8742 (m) cc_final: 0.8464 (p) REVERT: D 397 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7425 (pt0) REVERT: E 33 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8094 (mt) REVERT: E 198 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: E 449 LYS cc_start: 0.7615 (ttpt) cc_final: 0.7195 (ttmm) outliers start: 27 outliers final: 14 residues processed: 208 average time/residue: 1.1673 time to fit residues: 275.3216 Evaluate side-chains 201 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain F residue 14 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 122 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 310 ASN C 466 ASN E 439 ASN E 474 GLN G 10 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.087059 restraints weight = 21222.810| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.85 r_work: 0.2969 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18559 Z= 0.163 Angle : 0.601 7.083 25342 Z= 0.306 Chirality : 0.045 0.186 2990 Planarity : 0.004 0.048 3080 Dihedral : 9.166 101.400 3066 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 1.70 % Allowed : 10.41 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2142 helix: 2.56 (0.18), residues: 784 sheet: 0.73 (0.23), residues: 485 loop : -0.49 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.007 0.001 HIS D 408 PHE 0.015 0.002 PHE E 467 TYR 0.015 0.002 TYR G 25 ARG 0.003 0.000 ARG E 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 8) link_NAG-ASN : angle 1.99741 ( 24) link_ALPHA1-6 : bond 0.00455 ( 6) link_ALPHA1-6 : angle 1.48872 ( 18) link_BETA1-4 : bond 0.00396 ( 10) link_BETA1-4 : angle 2.56704 ( 30) link_ALPHA1-2 : bond 0.00599 ( 4) link_ALPHA1-2 : angle 2.15354 ( 12) link_ALPHA1-3 : bond 0.00783 ( 4) link_ALPHA1-3 : angle 1.30446 ( 12) hydrogen bonds : bond 0.06304 ( 852) hydrogen bonds : angle 4.42425 ( 2700) SS BOND : bond 0.00365 ( 14) SS BOND : angle 0.95995 ( 28) covalent geometry : bond 0.00375 (18512) covalent geometry : angle 0.58772 (25218) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 2.180 Fit side-chains REVERT: A 193 CYS cc_start: 0.8463 (m) cc_final: 0.7253 (p) REVERT: A 224 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8705 (tt) REVERT: A 386 MET cc_start: 0.8388 (mtp) cc_final: 0.8130 (mtm) REVERT: B 33 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 92 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8396 (mt) REVERT: C 13 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: C 194 ARG cc_start: 0.8843 (ptm160) cc_final: 0.8246 (ptp-170) REVERT: C 452 PHE cc_start: 0.7998 (m-80) cc_final: 0.7367 (t80) REVERT: D 191 THR cc_start: 0.8727 (m) cc_final: 0.8454 (p) REVERT: D 229 THR cc_start: 0.8059 (m) cc_final: 0.7667 (m) REVERT: D 397 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7454 (pt0) REVERT: E 14 ASP cc_start: 0.8206 (m-30) cc_final: 0.7800 (p0) REVERT: E 33 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8100 (pt) REVERT: E 449 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7348 (ttmm) outliers start: 34 outliers final: 18 residues processed: 200 average time/residue: 1.2072 time to fit residues: 274.7737 Evaluate side-chains 197 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 23 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 79 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS C 310 ASN C 466 ASN G 10 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.090814 restraints weight = 21414.829| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.86 r_work: 0.3027 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18559 Z= 0.109 Angle : 0.524 7.086 25342 Z= 0.267 Chirality : 0.042 0.201 2990 Planarity : 0.004 0.048 3080 Dihedral : 8.593 98.038 3066 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.00 % Allowed : 11.21 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 2142 helix: 2.78 (0.18), residues: 785 sheet: 0.81 (0.23), residues: 484 loop : -0.38 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 311 HIS 0.006 0.001 HIS D 408 PHE 0.011 0.001 PHE B 294 TYR 0.018 0.001 TYR F 25 ARG 0.002 0.000 ARG B 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 8) link_NAG-ASN : angle 1.83477 ( 24) link_ALPHA1-6 : bond 0.00593 ( 6) link_ALPHA1-6 : angle 1.46246 ( 18) link_BETA1-4 : bond 0.00447 ( 10) link_BETA1-4 : angle 2.08872 ( 30) link_ALPHA1-2 : bond 0.00429 ( 4) link_ALPHA1-2 : angle 1.81973 ( 12) link_ALPHA1-3 : bond 0.00896 ( 4) link_ALPHA1-3 : angle 1.26077 ( 12) hydrogen bonds : bond 0.05154 ( 852) hydrogen bonds : angle 4.15547 ( 2700) SS BOND : bond 0.00250 ( 14) SS BOND : angle 0.61629 ( 28) covalent geometry : bond 0.00222 (18512) covalent geometry : angle 0.51306 (25218) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 1.911 Fit side-chains REVERT: A 193 CYS cc_start: 0.8413 (m) cc_final: 0.7180 (p) REVERT: A 224 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8645 (tt) REVERT: A 324 MET cc_start: 0.4828 (tpt) cc_final: 0.4526 (tpp) REVERT: A 386 MET cc_start: 0.8340 (mtp) cc_final: 0.8089 (mtm) REVERT: B 33 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 92 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8365 (mt) REVERT: B 241 PHE cc_start: 0.8321 (m-10) cc_final: 0.6699 (t80) REVERT: C 13 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: C 194 ARG cc_start: 0.8733 (ptm160) cc_final: 0.8133 (ptp-170) REVERT: C 452 PHE cc_start: 0.8048 (m-80) cc_final: 0.7412 (t80) REVERT: D 191 THR cc_start: 0.8743 (m) cc_final: 0.8460 (p) REVERT: E 14 ASP cc_start: 0.8195 (m-30) cc_final: 0.7872 (p0) REVERT: E 33 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8130 (mt) REVERT: E 180 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8136 (mm-30) REVERT: E 449 LYS cc_start: 0.7598 (ttpt) cc_final: 0.7195 (ttmm) outliers start: 20 outliers final: 13 residues processed: 201 average time/residue: 1.2026 time to fit residues: 273.6758 Evaluate side-chains 200 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain F residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 56 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 123 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 ASN G 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089591 restraints weight = 21262.778| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.85 r_work: 0.3007 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18559 Z= 0.122 Angle : 0.550 7.205 25342 Z= 0.279 Chirality : 0.043 0.187 2990 Planarity : 0.004 0.048 3080 Dihedral : 8.627 97.849 3066 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.15 % Allowed : 11.36 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.18), residues: 2142 helix: 2.74 (0.18), residues: 784 sheet: 0.80 (0.23), residues: 484 loop : -0.37 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 311 HIS 0.011 0.001 HIS A 408 PHE 0.013 0.001 PHE B 473 TYR 0.018 0.001 TYR G 25 ARG 0.003 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 8) link_NAG-ASN : angle 1.86836 ( 24) link_ALPHA1-6 : bond 0.00532 ( 6) link_ALPHA1-6 : angle 1.46732 ( 18) link_BETA1-4 : bond 0.00396 ( 10) link_BETA1-4 : angle 2.23021 ( 30) link_ALPHA1-2 : bond 0.00436 ( 4) link_ALPHA1-2 : angle 1.94624 ( 12) link_ALPHA1-3 : bond 0.00844 ( 4) link_ALPHA1-3 : angle 1.28687 ( 12) hydrogen bonds : bond 0.05462 ( 852) hydrogen bonds : angle 4.20882 ( 2700) SS BOND : bond 0.00286 ( 14) SS BOND : angle 0.74472 ( 28) covalent geometry : bond 0.00264 (18512) covalent geometry : angle 0.53902 (25218) Misc. bond : bond 0.00030 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 2.018 Fit side-chains REVERT: A 193 CYS cc_start: 0.8446 (m) cc_final: 0.7212 (p) REVERT: A 224 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8648 (tt) REVERT: A 386 MET cc_start: 0.8371 (mtp) cc_final: 0.8120 (mtm) REVERT: B 33 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8446 (mp) REVERT: B 92 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8374 (mt) REVERT: B 241 PHE cc_start: 0.8318 (m-10) cc_final: 0.6698 (t80) REVERT: C 13 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: C 167 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: C 194 ARG cc_start: 0.8771 (ptm160) cc_final: 0.8163 (ptp-170) REVERT: C 452 PHE cc_start: 0.8048 (m-80) cc_final: 0.7415 (t80) REVERT: D 191 THR cc_start: 0.8742 (m) cc_final: 0.8455 (p) REVERT: D 397 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7422 (pt0) REVERT: E 14 ASP cc_start: 0.8180 (m-30) cc_final: 0.7883 (p0) REVERT: E 33 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8156 (mt) REVERT: E 180 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8112 (mm-30) REVERT: E 314 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.7095 (m) REVERT: E 449 LYS cc_start: 0.7679 (ttpt) cc_final: 0.7269 (ttmm) outliers start: 23 outliers final: 14 residues processed: 196 average time/residue: 1.1780 time to fit residues: 261.9920 Evaluate side-chains 200 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 130 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 93 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 ASN G 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091405 restraints weight = 21328.498| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.86 r_work: 0.3036 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18559 Z= 0.108 Angle : 0.523 6.606 25342 Z= 0.265 Chirality : 0.042 0.208 2990 Planarity : 0.004 0.047 3080 Dihedral : 8.334 95.510 3066 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.10 % Allowed : 11.36 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 2142 helix: 2.82 (0.18), residues: 784 sheet: 0.81 (0.23), residues: 484 loop : -0.31 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 311 HIS 0.007 0.001 HIS A 408 PHE 0.011 0.001 PHE E 467 TYR 0.020 0.001 TYR G 25 ARG 0.003 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 8) link_NAG-ASN : angle 1.77580 ( 24) link_ALPHA1-6 : bond 0.00595 ( 6) link_ALPHA1-6 : angle 1.48031 ( 18) link_BETA1-4 : bond 0.00436 ( 10) link_BETA1-4 : angle 2.01963 ( 30) link_ALPHA1-2 : bond 0.00383 ( 4) link_ALPHA1-2 : angle 1.81384 ( 12) link_ALPHA1-3 : bond 0.00863 ( 4) link_ALPHA1-3 : angle 1.27672 ( 12) hydrogen bonds : bond 0.05018 ( 852) hydrogen bonds : angle 4.09792 ( 2700) SS BOND : bond 0.00242 ( 14) SS BOND : angle 0.63359 ( 28) covalent geometry : bond 0.00223 (18512) covalent geometry : angle 0.51249 (25218) Misc. bond : bond 0.00026 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16969.70 seconds wall clock time: 294 minutes 42.67 seconds (17682.67 seconds total)