Starting phenix.real_space_refine on Thu Sep 18 15:40:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqn_39500/09_2025/8yqn_39500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqn_39500/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yqn_39500/09_2025/8yqn_39500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqn_39500/09_2025/8yqn_39500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yqn_39500/09_2025/8yqn_39500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqn_39500/09_2025/8yqn_39500.map" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.33, per 1000 atoms: 0.24 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: 2.04 Conformation dependent library (CDL) restraints added in 699.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.66 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: 3.18 Time building geometry restraints manager: 2.61 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.390 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.560 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.025 0.003 ARG C 319 TYR 0.032 0.002 TYR D 93 PHE 0.030 0.002 PHE E 422 TRP 0.023 0.002 TRP D 67 HIS 0.013 0.002 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00626 (18512) covalent geometry : angle 0.89919 (25218) SS BOND : bond 0.00916 ( 14) SS BOND : angle 2.20424 ( 28) hydrogen bonds : bond 0.14625 ( 852) hydrogen bonds : angle 6.57080 ( 2700) Misc. bond : bond 0.00326 ( 1) 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) 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_NAG-ASN : bond 0.00818 ( 8) link_NAG-ASN : angle 3.02028 ( 24) *********************** 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 : 0.744 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: 0.7311 time to fit residues: 181.3327 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 : 0.710 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 98 ASN B 103 HIS B 200 ASN 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 271 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090059 restraints weight = 21426.666| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.88 r_work: 0.3001 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18559 Z= 0.135 Angle : 0.615 8.379 25342 Z= 0.315 Chirality : 0.045 0.159 2990 Planarity : 0.005 0.042 3080 Dihedral : 11.732 120.847 3067 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.40 % Allowed : 6.16 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.17), residues: 2142 helix: 1.02 (0.18), residues: 783 sheet: -0.18 (0.22), residues: 466 loop : -1.17 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 455 TYR 0.013 0.001 TYR D 93 PHE 0.017 0.001 PHE A 284 TRP 0.012 0.001 TRP D 67 HIS 0.009 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00282 (18512) covalent geometry : angle 0.60113 (25218) SS BOND : bond 0.00308 ( 14) SS BOND : angle 1.04849 ( 28) hydrogen bonds : bond 0.06201 ( 852) hydrogen bonds : angle 4.67285 ( 2700) Misc. bond : bond 0.00030 ( 1) link_ALPHA1-2 : bond 0.00631 ( 4) link_ALPHA1-2 : angle 2.57034 ( 12) link_ALPHA1-3 : bond 0.00849 ( 4) link_ALPHA1-3 : angle 1.28825 ( 12) link_ALPHA1-6 : bond 0.00504 ( 6) link_ALPHA1-6 : angle 1.46974 ( 18) link_BETA1-4 : bond 0.00508 ( 10) link_BETA1-4 : angle 2.66255 ( 30) link_NAG-ASN : bond 0.00242 ( 8) link_NAG-ASN : angle 2.06734 ( 24) *********************** 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 227 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.873 Fit side-chains REVERT: C 452 PHE cc_start: 0.7971 (m-80) cc_final: 0.7300 (t80) REVERT: D 77 LYS cc_start: 0.8769 (mttm) cc_final: 0.8521 (mtmt) REVERT: D 229 THR cc_start: 0.8003 (m) cc_final: 0.7604 (m) REVERT: D 397 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7435 (pt0) REVERT: E 33 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8090 (pt) REVERT: E 449 LYS cc_start: 0.7669 (ttpt) cc_final: 0.7260 (tptp) REVERT: G 47 LYS cc_start: 0.7191 (mttt) cc_final: 0.6946 (mttt) outliers start: 28 outliers final: 9 residues processed: 213 average time/residue: 0.6920 time to fit residues: 164.4350 Evaluate side-chains 190 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 193 CYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 267 GLN B 313 HIS C 310 ASN E 188 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 = 0.3493 r_free = 0.3493 target = 0.115717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.086253 restraints weight = 21481.216| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.85 r_work: 0.2958 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18559 Z= 0.210 Angle : 0.685 9.748 25342 Z= 0.350 Chirality : 0.048 0.176 2990 Planarity : 0.005 0.045 3080 Dihedral : 10.702 116.091 3066 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 2.00 % Allowed : 6.56 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.18), residues: 2142 helix: 1.78 (0.18), residues: 781 sheet: 0.32 (0.23), residues: 462 loop : -0.89 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 223 TYR 0.025 0.002 TYR D 93 PHE 0.020 0.002 PHE E 467 TRP 0.014 0.002 TRP B 176 HIS 0.008 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00498 (18512) covalent geometry : angle 0.66888 (25218) SS BOND : bond 0.00446 ( 14) SS BOND : angle 1.28252 ( 28) hydrogen bonds : bond 0.07261 ( 852) hydrogen bonds : angle 4.68984 ( 2700) Misc. bond : bond 0.00005 ( 1) link_ALPHA1-2 : bond 0.00913 ( 4) link_ALPHA1-2 : angle 2.72396 ( 12) link_ALPHA1-3 : bond 0.00820 ( 4) link_ALPHA1-3 : angle 1.55981 ( 12) link_ALPHA1-6 : bond 0.00457 ( 6) link_ALPHA1-6 : angle 1.50315 ( 18) link_BETA1-4 : bond 0.00519 ( 10) link_BETA1-4 : angle 3.06769 ( 30) link_NAG-ASN : bond 0.00268 ( 8) link_NAG-ASN : angle 2.18991 ( 24) *********************** 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 220 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.751 Fit side-chains REVERT: A 329 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.5842 (mmm) REVERT: B 33 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8529 (mp) REVERT: C 13 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: C 194 ARG cc_start: 0.8882 (ptm160) cc_final: 0.8418 (ptp-170) REVERT: C 452 PHE cc_start: 0.7960 (m-80) cc_final: 0.7314 (t80) REVERT: D 77 LYS cc_start: 0.8857 (mttm) cc_final: 0.8656 (mtmt) REVERT: D 115 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8316 (mtpp) REVERT: D 320 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.6888 (mm) REVERT: D 397 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7468 (pt0) REVERT: E 33 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8142 (pt) REVERT: E 449 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7390 (tptp) outliers start: 40 outliers final: 15 residues processed: 202 average time/residue: 0.6561 time to fit residues: 148.6596 Evaluate side-chains 193 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 329 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 33 ILE 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 C residue 181 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 115 LYS 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 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 123 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 105 optimal weight: 0.0970 chunk 101 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 305 ASN B 313 HIS B 447 ASN C 196 ASN C 310 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089950 restraints weight = 21472.809| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.86 r_work: 0.3019 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18559 Z= 0.120 Angle : 0.548 6.912 25342 Z= 0.280 Chirality : 0.043 0.183 2990 Planarity : 0.004 0.042 3080 Dihedral : 9.587 109.432 3066 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 1.30 % Allowed : 8.66 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.18), residues: 2142 helix: 2.25 (0.18), residues: 785 sheet: 0.62 (0.23), residues: 462 loop : -0.66 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 455 TYR 0.012 0.001 TYR G 25 PHE 0.011 0.001 PHE E 467 TRP 0.013 0.001 TRP A 187 HIS 0.006 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00250 (18512) covalent geometry : angle 0.53533 (25218) SS BOND : bond 0.00264 ( 14) SS BOND : angle 0.75187 ( 28) hydrogen bonds : bond 0.05669 ( 852) hydrogen bonds : angle 4.31073 ( 2700) Misc. bond : bond 0.00043 ( 1) link_ALPHA1-2 : bond 0.01122 ( 4) link_ALPHA1-2 : angle 1.90506 ( 12) link_ALPHA1-3 : bond 0.00941 ( 4) link_ALPHA1-3 : angle 1.16365 ( 12) link_ALPHA1-6 : bond 0.00550 ( 6) link_ALPHA1-6 : angle 1.43206 ( 18) link_BETA1-4 : bond 0.00454 ( 10) link_BETA1-4 : angle 2.44505 ( 30) link_NAG-ASN : bond 0.00245 ( 8) link_NAG-ASN : angle 1.94422 ( 24) *********************** 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 219 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.581 Fit side-chains REVERT: B 33 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8387 (mt) REVERT: C 13 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: C 194 ARG cc_start: 0.8820 (ptm160) cc_final: 0.8373 (ptp-170) REVERT: C 196 ASN cc_start: 0.8587 (m110) cc_final: 0.8306 (m110) REVERT: C 452 PHE cc_start: 0.8042 (m-80) cc_final: 0.7402 (t80) REVERT: D 229 THR cc_start: 0.7846 (m) cc_final: 0.7380 (m) REVERT: D 308 MET cc_start: 0.8918 (tpp) cc_final: 0.8588 (tpp) REVERT: D 397 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7466 (pt0) REVERT: E 33 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8026 (pt) REVERT: E 198 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: E 449 LYS cc_start: 0.7692 (ttpt) cc_final: 0.7289 (ttmm) outliers start: 26 outliers final: 10 residues processed: 210 average time/residue: 0.6252 time to fit residues: 146.9260 Evaluate side-chains 195 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 416 LEU Chi-restraints excluded: chain B residue 33 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 193 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 33 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 163 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 305 ASN B 427 ASN B 447 ASN C 119 GLN C 310 ASN C 466 ASN E 181 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.085610 restraints weight = 21321.918| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.85 r_work: 0.2948 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18559 Z= 0.216 Angle : 0.666 6.897 25342 Z= 0.341 Chirality : 0.048 0.191 2990 Planarity : 0.005 0.045 3080 Dihedral : 9.988 107.945 3066 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 2.25 % Allowed : 8.11 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.18), residues: 2142 helix: 2.13 (0.18), residues: 784 sheet: 0.57 (0.23), residues: 487 loop : -0.69 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 217 TYR 0.017 0.002 TYR B 202 PHE 0.019 0.002 PHE E 467 TRP 0.014 0.002 TRP B 176 HIS 0.006 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00513 (18512) covalent geometry : angle 0.65137 (25218) SS BOND : bond 0.00450 ( 14) SS BOND : angle 1.22152 ( 28) hydrogen bonds : bond 0.07215 ( 852) hydrogen bonds : angle 4.63482 ( 2700) Misc. bond : bond 0.00020 ( 1) link_ALPHA1-2 : bond 0.00953 ( 4) link_ALPHA1-2 : angle 2.38365 ( 12) link_ALPHA1-3 : bond 0.00783 ( 4) link_ALPHA1-3 : angle 1.44062 ( 12) link_ALPHA1-6 : bond 0.00444 ( 6) link_ALPHA1-6 : angle 1.52656 ( 18) link_BETA1-4 : bond 0.00441 ( 10) link_BETA1-4 : angle 2.95345 ( 30) link_NAG-ASN : bond 0.00238 ( 8) link_NAG-ASN : angle 2.16883 ( 24) *********************** 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 224 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 179 time to evaluate : 0.728 Fit side-chains REVERT: A 193 CYS cc_start: 0.8538 (m) cc_final: 0.7353 (p) REVERT: A 386 MET cc_start: 0.8396 (mtp) cc_final: 0.8183 (mtm) REVERT: B 33 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8493 (mp) REVERT: B 92 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8437 (mt) REVERT: C 13 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: C 194 ARG cc_start: 0.8903 (ptm160) cc_final: 0.8471 (ptp-170) REVERT: C 452 PHE cc_start: 0.7896 (m-80) cc_final: 0.7259 (t80) REVERT: D 320 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.6909 (mm) REVERT: D 397 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7447 (pt0) REVERT: E 33 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8122 (pt) REVERT: E 449 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7372 (ttmm) outliers start: 45 outliers final: 24 residues processed: 209 average time/residue: 0.6303 time to fit residues: 148.7304 Evaluate side-chains 200 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 274 ILE 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 60 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 298 LEU 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 284 LEU 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 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 174 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 305 ASN C 95 ASN C 310 ASN E 99 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.087584 restraints weight = 21164.877| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.84 r_work: 0.2980 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18559 Z= 0.143 Angle : 0.575 6.567 25342 Z= 0.295 Chirality : 0.044 0.168 2990 Planarity : 0.004 0.047 3080 Dihedral : 9.496 104.402 3066 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.15 % Rotamer: Outliers : 1.65 % Allowed : 9.21 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.18), residues: 2142 helix: 2.41 (0.18), residues: 783 sheet: 0.65 (0.23), residues: 484 loop : -0.61 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 55 TYR 0.013 0.001 TYR B 439 PHE 0.015 0.001 PHE B 473 TRP 0.013 0.001 TRP A 187 HIS 0.006 0.001 HIS D 408 Details of bonding type rmsd covalent geometry : bond 0.00316 (18512) covalent geometry : angle 0.56190 (25218) SS BOND : bond 0.00326 ( 14) SS BOND : angle 0.88844 ( 28) hydrogen bonds : bond 0.06188 ( 852) hydrogen bonds : angle 4.43313 ( 2700) Misc. bond : bond 0.00035 ( 1) link_ALPHA1-2 : bond 0.00675 ( 4) link_ALPHA1-2 : angle 2.02610 ( 12) link_ALPHA1-3 : bond 0.00828 ( 4) link_ALPHA1-3 : angle 1.20736 ( 12) link_ALPHA1-6 : bond 0.00486 ( 6) link_ALPHA1-6 : angle 1.45801 ( 18) link_BETA1-4 : bond 0.00418 ( 10) link_BETA1-4 : angle 2.54660 ( 30) link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 2.02481 ( 24) *********************** 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 217 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.678 Fit side-chains REVERT: A 193 CYS cc_start: 0.8511 (m) cc_final: 0.7236 (p) REVERT: B 33 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8444 (mp) REVERT: B 92 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8414 (mt) REVERT: C 13 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: C 194 ARG cc_start: 0.8864 (ptm160) cc_final: 0.8409 (ptp-170) REVERT: C 196 ASN cc_start: 0.8735 (m110) cc_final: 0.8429 (m110) REVERT: C 452 PHE cc_start: 0.8058 (m-80) cc_final: 0.7429 (t80) REVERT: D 391 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: D 397 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7484 (pt0) REVERT: E 14 ASP cc_start: 0.8221 (m-30) cc_final: 0.7782 (p0) REVERT: E 33 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8072 (pt) REVERT: E 198 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: E 449 LYS cc_start: 0.7719 (ttpt) cc_final: 0.7307 (ttmm) outliers start: 33 outliers final: 18 residues processed: 204 average time/residue: 0.6451 time to fit residues: 148.0099 Evaluate side-chains 200 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 274 ILE 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 112 VAL 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 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 132 VAL Chi-restraints excluded: chain E residue 198 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 464 LEU 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 206 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 305 ASN C 310 ASN E 271 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.086512 restraints weight = 21356.674| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.85 r_work: 0.2963 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18559 Z= 0.172 Angle : 0.610 6.518 25342 Z= 0.312 Chirality : 0.046 0.179 2990 Planarity : 0.005 0.046 3080 Dihedral : 9.551 103.817 3066 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 1.70 % Allowed : 9.26 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.18), residues: 2142 helix: 2.38 (0.18), residues: 783 sheet: 0.64 (0.23), residues: 485 loop : -0.59 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 217 TYR 0.018 0.002 TYR F 25 PHE 0.015 0.002 PHE E 467 TRP 0.011 0.001 TRP B 176 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00398 (18512) covalent geometry : angle 0.59612 (25218) SS BOND : bond 0.00380 ( 14) SS BOND : angle 1.02380 ( 28) hydrogen bonds : bond 0.06584 ( 852) hydrogen bonds : angle 4.50556 ( 2700) Misc. bond : bond 0.00026 ( 1) link_ALPHA1-2 : bond 0.00712 ( 4) link_ALPHA1-2 : angle 2.18375 ( 12) link_ALPHA1-3 : bond 0.00801 ( 4) link_ALPHA1-3 : angle 1.29531 ( 12) link_ALPHA1-6 : bond 0.00451 ( 6) link_ALPHA1-6 : angle 1.48515 ( 18) link_BETA1-4 : bond 0.00409 ( 10) link_BETA1-4 : angle 2.68328 ( 30) link_NAG-ASN : bond 0.00218 ( 8) link_NAG-ASN : angle 2.07479 ( 24) *********************** 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 210 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.806 Fit side-chains REVERT: A 193 CYS cc_start: 0.8479 (m) cc_final: 0.7255 (p) REVERT: A 224 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8723 (tt) REVERT: B 33 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8451 (mp) REVERT: B 92 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8412 (mt) REVERT: C 13 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: C 194 ARG cc_start: 0.8874 (ptm160) cc_final: 0.8416 (ptp-170) REVERT: C 452 PHE cc_start: 0.8003 (m-80) cc_final: 0.7375 (t80) REVERT: D 320 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6901 (mm) REVERT: D 391 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: D 397 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7423 (pt0) REVERT: E 14 ASP cc_start: 0.8237 (m-30) cc_final: 0.7801 (p0) REVERT: E 33 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8116 (pt) REVERT: E 198 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: E 449 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7405 (ttmm) outliers start: 34 outliers final: 20 residues processed: 199 average time/residue: 0.6335 time to fit residues: 142.2031 Evaluate side-chains 200 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 274 ILE 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 112 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 THR 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 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 132 VAL Chi-restraints excluded: chain E residue 198 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 6 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 204 optimal weight: 0.0870 chunk 181 optimal weight: 0.9980 chunk 129 optimal weight: 0.2980 chunk 201 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS B 305 ASN C 310 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091455 restraints weight = 21259.459| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.84 r_work: 0.3040 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1942 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= 0.108 Angle : 0.519 6.615 25342 Z= 0.265 Chirality : 0.042 0.207 2990 Planarity : 0.004 0.047 3080 Dihedral : 8.781 99.050 3066 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 1.20 % Allowed : 10.21 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.19), residues: 2142 helix: 2.69 (0.18), residues: 785 sheet: 0.74 (0.23), residues: 484 loop : -0.41 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 55 TYR 0.013 0.001 TYR B 439 PHE 0.011 0.001 PHE B 294 TRP 0.016 0.001 TRP D 187 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00219 (18512) covalent geometry : angle 0.50776 (25218) SS BOND : bond 0.00233 ( 14) SS BOND : angle 0.62466 ( 28) hydrogen bonds : bond 0.05133 ( 852) hydrogen bonds : angle 4.15580 ( 2700) Misc. bond : bond 0.00040 ( 1) link_ALPHA1-2 : bond 0.00492 ( 4) link_ALPHA1-2 : angle 1.76007 ( 12) link_ALPHA1-3 : bond 0.00901 ( 4) link_ALPHA1-3 : angle 1.22463 ( 12) link_ALPHA1-6 : bond 0.00594 ( 6) link_ALPHA1-6 : angle 1.45532 ( 18) link_BETA1-4 : bond 0.00447 ( 10) link_BETA1-4 : angle 2.07628 ( 30) link_NAG-ASN : bond 0.00213 ( 8) link_NAG-ASN : angle 1.83684 ( 24) *********************** 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 214 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.755 Fit side-chains REVERT: A 193 CYS cc_start: 0.8432 (m) cc_final: 0.7152 (p) REVERT: A 224 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 324 MET cc_start: 0.4957 (tpt) cc_final: 0.4669 (tpp) REVERT: A 386 MET cc_start: 0.8319 (mtp) cc_final: 0.8031 (mtm) REVERT: A 394 ASN cc_start: 0.8140 (m-40) cc_final: 0.7878 (m-40) REVERT: B 33 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8298 (mt) REVERT: B 92 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8333 (mp) REVERT: C 13 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: C 194 ARG cc_start: 0.8778 (ptm160) cc_final: 0.8325 (ptp-170) REVERT: C 452 PHE cc_start: 0.8035 (m-80) cc_final: 0.7402 (t80) REVERT: D 191 THR cc_start: 0.8741 (m) cc_final: 0.8463 (p) REVERT: D 391 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: E 14 ASP cc_start: 0.8190 (m-30) cc_final: 0.7874 (p0) REVERT: E 33 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8077 (mt) REVERT: E 449 LYS cc_start: 0.7649 (ttpt) cc_final: 0.7238 (ttmm) outliers start: 24 outliers final: 11 residues processed: 203 average time/residue: 0.6210 time to fit residues: 142.1515 Evaluate side-chains 201 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 188 optimal weight: 0.0970 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS C 466 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088432 restraints weight = 21282.842| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.85 r_work: 0.2992 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18559 Z= 0.141 Angle : 0.573 7.876 25342 Z= 0.292 Chirality : 0.044 0.171 2990 Planarity : 0.004 0.047 3080 Dihedral : 9.008 99.580 3066 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 1.10 % Allowed : 10.76 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.18), residues: 2142 helix: 2.63 (0.18), residues: 784 sheet: 0.76 (0.23), residues: 484 loop : -0.41 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 55 TYR 0.018 0.002 TYR G 25 PHE 0.015 0.001 PHE B 473 TRP 0.011 0.001 TRP D 311 HIS 0.006 0.001 HIS D 408 Details of bonding type rmsd covalent geometry : bond 0.00317 (18512) covalent geometry : angle 0.56089 (25218) SS BOND : bond 0.00328 ( 14) SS BOND : angle 0.86351 ( 28) hydrogen bonds : bond 0.05877 ( 852) hydrogen bonds : angle 4.31094 ( 2700) Misc. bond : bond 0.00027 ( 1) link_ALPHA1-2 : bond 0.00529 ( 4) link_ALPHA1-2 : angle 2.04405 ( 12) link_ALPHA1-3 : bond 0.00819 ( 4) link_ALPHA1-3 : angle 1.29256 ( 12) link_ALPHA1-6 : bond 0.00494 ( 6) link_ALPHA1-6 : angle 1.47046 ( 18) link_BETA1-4 : bond 0.00378 ( 10) link_BETA1-4 : angle 2.40960 ( 30) link_NAG-ASN : bond 0.00187 ( 8) link_NAG-ASN : angle 1.93630 ( 24) *********************** 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 201 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.881 Fit side-chains REVERT: A 193 CYS cc_start: 0.8447 (m) cc_final: 0.7191 (p) REVERT: A 224 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8692 (tt) REVERT: B 33 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8408 (mt) REVERT: B 92 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8401 (mt) REVERT: C 13 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: C 194 ARG cc_start: 0.8834 (ptm160) cc_final: 0.8377 (ptp-170) REVERT: C 452 PHE cc_start: 0.8044 (m-80) cc_final: 0.7417 (t80) REVERT: D 229 THR cc_start: 0.7943 (m) cc_final: 0.7453 (m) REVERT: D 391 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: D 397 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7484 (pt0) REVERT: E 14 ASP cc_start: 0.8196 (m-30) cc_final: 0.7891 (p0) REVERT: E 33 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8143 (mt) REVERT: E 449 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7313 (ttmm) outliers start: 22 outliers final: 11 residues processed: 196 average time/residue: 0.6473 time to fit residues: 142.7940 Evaluate side-chains 194 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 211 optimal weight: 0.2980 chunk 197 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089651 restraints weight = 21213.575| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.85 r_work: 0.3009 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18559 Z= 0.121 Angle : 0.546 6.898 25342 Z= 0.278 Chirality : 0.043 0.184 2990 Planarity : 0.004 0.046 3080 Dihedral : 8.832 97.910 3066 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.00 % Allowed : 10.91 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.18), residues: 2142 helix: 2.69 (0.18), residues: 785 sheet: 0.78 (0.23), residues: 484 loop : -0.36 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 55 TYR 0.020 0.001 TYR G 25 PHE 0.012 0.001 PHE B 294 TRP 0.012 0.001 TRP D 311 HIS 0.007 0.001 HIS D 408 Details of bonding type rmsd covalent geometry : bond 0.00260 (18512) covalent geometry : angle 0.53474 (25218) SS BOND : bond 0.00275 ( 14) SS BOND : angle 0.71833 ( 28) hydrogen bonds : bond 0.05511 ( 852) hydrogen bonds : angle 4.24186 ( 2700) Misc. bond : bond 0.00030 ( 1) link_ALPHA1-2 : bond 0.00432 ( 4) link_ALPHA1-2 : angle 1.93362 ( 12) link_ALPHA1-3 : bond 0.00839 ( 4) link_ALPHA1-3 : angle 1.25617 ( 12) link_ALPHA1-6 : bond 0.00527 ( 6) link_ALPHA1-6 : angle 1.46296 ( 18) link_BETA1-4 : bond 0.00413 ( 10) link_BETA1-4 : angle 2.23538 ( 30) link_NAG-ASN : bond 0.00196 ( 8) link_NAG-ASN : angle 1.87229 ( 24) ********************** 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 209 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.748 Fit side-chains REVERT: A 193 CYS cc_start: 0.8415 (m) cc_final: 0.7171 (p) REVERT: A 224 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 324 MET cc_start: 0.4767 (tpt) cc_final: 0.4415 (tpp) REVERT: B 33 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8386 (mt) REVERT: B 92 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8358 (mp) REVERT: C 13 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: C 194 ARG cc_start: 0.8811 (ptm160) cc_final: 0.8360 (ptp-170) REVERT: C 452 PHE cc_start: 0.8043 (m-80) cc_final: 0.7422 (t80) REVERT: D 191 THR cc_start: 0.8746 (m) cc_final: 0.8461 (p) REVERT: D 391 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: E 14 ASP cc_start: 0.8190 (m-30) cc_final: 0.7894 (p0) REVERT: E 33 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8102 (mt) REVERT: E 449 LYS cc_start: 0.7641 (ttpt) cc_final: 0.7247 (ttmm) outliers start: 20 outliers final: 13 residues processed: 204 average time/residue: 0.6324 time to fit residues: 145.2703 Evaluate side-chains 202 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 112 VAL 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 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 59 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 137 optimal weight: 0.0070 chunk 109 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 205 optimal weight: 0.1980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN C 466 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092416 restraints weight = 21417.694| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.85 r_work: 0.3051 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2094 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= 0.104 Angle : 0.515 6.463 25342 Z= 0.262 Chirality : 0.042 0.218 2990 Planarity : 0.004 0.047 3080 Dihedral : 8.341 94.840 3066 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.95 % Allowed : 11.11 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.19), residues: 2142 helix: 2.84 (0.18), residues: 784 sheet: 0.90 (0.24), residues: 462 loop : -0.29 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 55 TYR 0.012 0.001 TYR B 439 PHE 0.011 0.001 PHE E 267 TRP 0.015 0.001 TRP D 311 HIS 0.006 0.001 HIS D 408 Details of bonding type rmsd covalent geometry : bond 0.00212 (18512) covalent geometry : angle 0.50433 (25218) SS BOND : bond 0.00227 ( 14) SS BOND : angle 0.62372 ( 28) hydrogen bonds : bond 0.04880 ( 852) hydrogen bonds : angle 4.05811 ( 2700) Misc. bond : bond 0.00024 ( 1) link_ALPHA1-2 : bond 0.00381 ( 4) link_ALPHA1-2 : angle 1.79382 ( 12) link_ALPHA1-3 : bond 0.00886 ( 4) link_ALPHA1-3 : angle 1.28253 ( 12) link_ALPHA1-6 : bond 0.00611 ( 6) link_ALPHA1-6 : angle 1.47868 ( 18) link_BETA1-4 : bond 0.00433 ( 10) link_BETA1-4 : angle 1.95173 ( 30) link_NAG-ASN : bond 0.00173 ( 8) link_NAG-ASN : angle 1.73359 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7952.22 seconds wall clock time: 136 minutes 2.98 seconds (8162.98 seconds total)