Starting phenix.real_space_refine on Thu Feb 5 09:44:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lhb_63092/02_2026/9lhb_63092.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lhb_63092/02_2026/9lhb_63092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lhb_63092/02_2026/9lhb_63092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lhb_63092/02_2026/9lhb_63092.map" model { file = "/net/cci-nas-00/data/ceres_data/9lhb_63092/02_2026/9lhb_63092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lhb_63092/02_2026/9lhb_63092.cif" } resolution = 3.11 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= 0.000 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10576 2.51 5 N 2613 2.21 5 O 2947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16251 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3274 Chain: "B" Number of atoms: 3207 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3200 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 400, 3200 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3280 Chain: "C" Number of atoms: 3201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3274 Chain: "D" Number of atoms: 3201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3274 Chain: "E" Number of atoms: 3205 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3198 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 400, 3198 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3278 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.37, per 1000 atoms: 0.39 Number of scatterers: 16251 At special positions: 0 Unit cell: (89.89, 92.92, 170.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 2947 8.00 N 2613 7.00 C 10576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 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=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 602 " - " ASN A 46 " " NAG B 602 " - " ASN B 46 " " NAG C 601 " - " ASN C 46 " " NAG D 601 " - " ASN D 46 " " NAG E 601 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 864.7 milliseconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 21 sheets defined 44.3% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.572A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 removed outlier: 5.132A pdb=" N ILE A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 260 through 283 removed outlier: 4.034A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 431 through 489 Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.794A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 237 through 249 removed outlier: 3.707A pdb=" N CYS B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 260 through 283 removed outlier: 3.786A pdb=" N LEU B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.877A pdb=" N TRP B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 431 through 490 removed outlier: 4.228A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.594A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 237 through 249 removed outlier: 3.586A pdb=" N LEU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.772A pdb=" N GLY C 259 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 280 Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 328 through 337 removed outlier: 3.588A pdb=" N ASN C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.587A pdb=" N TRP C 341 " --> pdb=" O ASN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 488 removed outlier: 3.812A pdb=" N LYS C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.727A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 249 removed outlier: 4.780A pdb=" N ILE D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 260 through 280 removed outlier: 3.590A pdb=" N LEU D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 328 through 335 Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 431 through 490 removed outlier: 3.719A pdb=" N VAL D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N CYS D 457 " --> pdb=" O SER D 453 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 502 removed outlier: 3.601A pdb=" N ALA D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.635A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 248 removed outlier: 4.849A pdb=" N ILE E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 249 through 252 Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 262 through 280 Processing helix chain 'E' and resid 291 through 319 Processing helix chain 'E' and resid 328 through 336 Processing helix chain 'E' and resid 337 through 344 removed outlier: 3.726A pdb=" N TRP E 341 " --> pdb=" O ASN E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 488 Processing helix chain 'E' and resid 492 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.604A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.604A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLN A 79 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER A 58 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N SER A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER A 56 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N THR A 83 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N TYR A 54 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 53 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.503A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.503A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 208 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 140 Processing sheet with id=AA6, first strand: chain 'B' and resid 137 through 140 removed outlier: 7.025A pdb=" N VAL B 71 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP B 64 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR B 73 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN B 75 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR B 83 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 52 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.702A pdb=" N VAL B 100 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.550A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.550A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 143 through 149 removed outlier: 7.138A pdb=" N VAL C 71 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP C 64 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 79 " --> pdb=" O SER C 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 removed outlier: 7.167A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.684A pdb=" N ASN D 75 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N TRP D 77 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU D 60 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLN D 79 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER D 58 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N SER D 81 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER D 56 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N THR D 83 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N TYR D 54 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 3.622A pdb=" N LEU D 113 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 220 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 112 through 114 removed outlier: 3.622A pdb=" N LEU D 113 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 220 " --> pdb=" O PHE D 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.530A pdb=" N GLY E 144 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.668A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N THR E 83 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N TYR E 54 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 161 through 168 removed outlier: 3.587A pdb=" N VAL E 220 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 161 through 168 removed outlier: 3.587A pdb=" N VAL E 220 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP E 219 " --> pdb=" O SER E 206 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2616 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: 2.46 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2569 1.32 - 1.45: 4720 1.45 - 1.58: 9243 1.58 - 1.71: 4 1.71 - 1.84: 170 Bond restraints: 16706 Sorted by residual: bond pdb=" C6 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" C6 NCT B 601 " pdb=" N2 NCT B 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" C6 NCT A 601 " pdb=" C7 NCT A 601 " ideal model delta sigma weight residual 1.536 1.369 0.167 2.00e-02 2.50e+03 6.97e+01 bond pdb=" C6 NCT B 601 " pdb=" C7 NCT B 601 " ideal model delta sigma weight residual 1.536 1.369 0.167 2.00e-02 2.50e+03 6.97e+01 bond pdb=" C9 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.306 0.146 2.00e-02 2.50e+03 5.30e+01 ... (remaining 16701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 22289 1.97 - 3.94: 403 3.94 - 5.91: 93 5.91 - 7.87: 8 7.87 - 9.84: 2 Bond angle restraints: 22795 Sorted by residual: angle pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" C5 NAG F 1 " ideal model delta sigma weight residual 109.38 119.22 -9.84 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CA GLU A 438 " pdb=" CB GLU A 438 " pdb=" CG GLU A 438 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N LEU C 336 " pdb=" CA LEU C 336 " pdb=" C LEU C 336 " ideal model delta sigma weight residual 112.38 116.22 -3.84 1.22e+00 6.72e-01 9.91e+00 angle pdb=" N ILE D 302 " pdb=" CA ILE D 302 " pdb=" CB ILE D 302 " ideal model delta sigma weight residual 110.77 116.31 -5.54 1.81e+00 3.05e-01 9.37e+00 angle pdb=" CB GLU A 438 " pdb=" CG GLU A 438 " pdb=" CD GLU A 438 " ideal model delta sigma weight residual 112.60 117.62 -5.02 1.70e+00 3.46e-01 8.73e+00 ... (remaining 22790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 8645 17.60 - 35.20: 1093 35.20 - 52.79: 254 52.79 - 70.39: 43 70.39 - 87.99: 15 Dihedral angle restraints: 10050 sinusoidal: 4155 harmonic: 5895 Sorted by residual: dihedral pdb=" CB CYS A 150 " pdb=" SG CYS A 150 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual 93.00 43.40 49.60 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CA CYS C 212 " pdb=" C CYS C 212 " pdb=" N CYS C 213 " pdb=" CA CYS C 213 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS C 150 " pdb=" SG CYS C 150 " pdb=" SG CYS C 164 " pdb=" CB CYS C 164 " ideal model delta sinusoidal sigma weight residual 93.00 50.24 42.76 1 1.00e+01 1.00e-02 2.55e+01 ... (remaining 10047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2055 0.048 - 0.096: 419 0.096 - 0.144: 108 0.144 - 0.192: 16 0.192 - 0.239: 4 Chirality restraints: 2602 Sorted by residual: chirality pdb=" CB VAL D 154 " pdb=" CA VAL D 154 " pdb=" CG1 VAL D 154 " pdb=" CG2 VAL D 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA LEU B 437 " pdb=" N LEU B 437 " pdb=" C LEU B 437 " pdb=" CB LEU B 437 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2599 not shown) Planarity restraints: 2848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 438 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" CD GLU C 438 " -0.064 2.00e-02 2.50e+03 pdb=" OE1 GLU C 438 " 0.023 2.00e-02 2.50e+03 pdb=" OE2 GLU C 438 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 205 " -0.275 9.50e-02 1.11e+02 1.23e-01 9.32e+00 pdb=" NE ARG D 205 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 205 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 205 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 205 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 215 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO C 216 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " 0.030 5.00e-02 4.00e+02 ... (remaining 2845 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1437 2.74 - 3.28: 15283 3.28 - 3.82: 26846 3.82 - 4.36: 29979 4.36 - 4.90: 53733 Nonbonded interactions: 127278 Sorted by model distance: nonbonded pdb=" OG SER E 206 " pdb=" OD1 ASP E 219 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP C 111 " pdb=" OG SER C 170 " model vdw 2.227 3.040 nonbonded pdb=" NH1 ARG B 347 " pdb=" O PRO B 348 " model vdw 2.230 3.120 nonbonded pdb=" OD2 ASP D 160 " pdb=" NH1 ARG D 228 " model vdw 2.292 3.120 nonbonded pdb=" OD2 ASP C 160 " pdb=" NH1 ARG C 228 " model vdw 2.295 3.120 ... (remaining 127273 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' and (resid 23 through 136 or resid 138 through 502)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 343 or (resid 344 and \ (name N or name CA or name C or name O or name CB )) or resid 345 through 502)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 502)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 502)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 345 or (resid 346 and \ (name N or name CA or name C or name O or name CB )) or resid 347 through 502)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.29 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.130 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.173 16731 Z= 0.363 Angle : 0.649 9.843 22860 Z= 0.304 Chirality : 0.043 0.239 2602 Planarity : 0.005 0.123 2838 Dihedral : 16.099 87.991 6210 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.23 % Allowed : 19.58 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.06 (0.19), residues: 1985 helix: 2.04 (0.18), residues: 822 sheet: 0.19 (0.27), residues: 387 loop : -0.44 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 448 TYR 0.017 0.001 TYR E 296 PHE 0.008 0.001 PHE C 157 TRP 0.029 0.001 TRP C 330 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00740 (16706) covalent geometry : angle 0.63786 (22795) SS BOND : bond 0.00706 ( 10) SS BOND : angle 1.61301 ( 20) hydrogen bonds : bond 0.14631 ( 833) hydrogen bonds : angle 5.86632 ( 2616) link_BETA1-4 : bond 0.00207 ( 5) link_BETA1-4 : angle 0.61257 ( 15) link_NAG-ASN : bond 0.00375 ( 10) link_NAG-ASN : angle 3.09745 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 296 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 432 ASP cc_start: 0.8640 (m-30) cc_final: 0.8319 (m-30) REVERT: A 441 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8351 (mtm-85) REVERT: C 275 PHE cc_start: 0.8594 (t80) cc_final: 0.8192 (t80) REVERT: C 342 PHE cc_start: 0.8304 (t80) cc_final: 0.8030 (m-10) REVERT: C 438 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: C 442 TYR cc_start: 0.8974 (t80) cc_final: 0.8678 (t80) REVERT: D 273 THR cc_start: 0.9229 (m) cc_final: 0.8822 (p) REVERT: D 435 LYS cc_start: 0.9502 (mmtp) cc_final: 0.9162 (mmtt) REVERT: D 438 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8442 (tm-30) REVERT: D 450 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8520 (tm-30) REVERT: D 451 ASP cc_start: 0.8664 (m-30) cc_final: 0.8394 (m-30) REVERT: D 481 ILE cc_start: 0.8891 (mm) cc_final: 0.8674 (tt) REVERT: E 120 GLU cc_start: 0.8289 (pm20) cc_final: 0.8088 (pm20) REVERT: E 176 TRP cc_start: 0.8298 (m-10) cc_final: 0.7927 (m-90) REVERT: E 296 TYR cc_start: 0.8452 (t80) cc_final: 0.8249 (t80) REVERT: E 321 ASP cc_start: 0.8567 (t0) cc_final: 0.8132 (t0) outliers start: 3 outliers final: 1 residues processed: 298 average time/residue: 0.1011 time to fit residues: 47.5600 Evaluate side-chains 246 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain C residue 438 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A A 163 HIS A 319 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.065950 restraints weight = 90742.412| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 5.08 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16731 Z= 0.148 Angle : 0.611 12.880 22860 Z= 0.300 Chirality : 0.043 0.461 2602 Planarity : 0.004 0.043 2838 Dihedral : 7.265 62.440 2512 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.09 % Allowed : 19.64 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.26 (0.19), residues: 1985 helix: 2.22 (0.18), residues: 819 sheet: 0.38 (0.26), residues: 393 loop : -0.41 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 469 TYR 0.019 0.001 TYR B 296 PHE 0.013 0.001 PHE C 146 TRP 0.033 0.001 TRP D 176 HIS 0.004 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00339 (16706) covalent geometry : angle 0.58745 (22795) SS BOND : bond 0.00843 ( 10) SS BOND : angle 2.23345 ( 20) hydrogen bonds : bond 0.04921 ( 833) hydrogen bonds : angle 4.44563 ( 2616) link_BETA1-4 : bond 0.00435 ( 5) link_BETA1-4 : angle 1.74669 ( 15) link_NAG-ASN : bond 0.00466 ( 10) link_NAG-ASN : angle 4.18134 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 MET cc_start: 0.8055 (ttp) cc_final: 0.7766 (ttt) REVERT: C 275 PHE cc_start: 0.8496 (t80) cc_final: 0.8022 (t80) REVERT: C 342 PHE cc_start: 0.8476 (t80) cc_final: 0.7952 (m-10) REVERT: C 442 TYR cc_start: 0.8890 (t80) cc_final: 0.8575 (t80) REVERT: C 450 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8549 (mm-40) REVERT: D 273 THR cc_start: 0.8882 (m) cc_final: 0.8615 (p) REVERT: D 435 LYS cc_start: 0.9428 (mmtp) cc_final: 0.9187 (mmtt) REVERT: D 450 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 451 ASP cc_start: 0.8647 (m-30) cc_final: 0.8409 (m-30) REVERT: D 454 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8629 (tp30) REVERT: D 481 ILE cc_start: 0.8633 (mm) cc_final: 0.8422 (tt) REVERT: E 120 GLU cc_start: 0.8510 (pm20) cc_final: 0.8184 (pm20) REVERT: E 176 TRP cc_start: 0.8417 (m-10) cc_final: 0.7915 (m-90) REVERT: E 296 TYR cc_start: 0.8206 (t80) cc_final: 0.7942 (t80) REVERT: E 321 ASP cc_start: 0.8587 (t0) cc_final: 0.7930 (t0) outliers start: 36 outliers final: 23 residues processed: 269 average time/residue: 0.0978 time to fit residues: 42.2417 Evaluate side-chains 264 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 481 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 86 optimal weight: 0.0000 chunk 95 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.065725 restraints weight = 83886.387| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.91 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16731 Z= 0.147 Angle : 0.585 9.849 22860 Z= 0.285 Chirality : 0.042 0.488 2602 Planarity : 0.004 0.039 2838 Dihedral : 6.022 55.553 2512 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 19.70 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.34 (0.19), residues: 1985 helix: 2.26 (0.18), residues: 825 sheet: 0.49 (0.26), residues: 393 loop : -0.39 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 469 TYR 0.019 0.001 TYR B 296 PHE 0.010 0.001 PHE C 146 TRP 0.021 0.001 TRP D 176 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00339 (16706) covalent geometry : angle 0.55900 (22795) SS BOND : bond 0.00828 ( 10) SS BOND : angle 2.19597 ( 20) hydrogen bonds : bond 0.04819 ( 833) hydrogen bonds : angle 4.19357 ( 2616) link_BETA1-4 : bond 0.00405 ( 5) link_BETA1-4 : angle 1.93864 ( 15) link_NAG-ASN : bond 0.00374 ( 10) link_NAG-ASN : angle 4.25053 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8793 (t0) cc_final: 0.8322 (t0) REVERT: A 283 MET cc_start: 0.8344 (mmp) cc_final: 0.8118 (mmm) REVERT: B 347 ARG cc_start: 0.8006 (tmt-80) cc_final: 0.7510 (tmt-80) REVERT: B 471 CYS cc_start: 0.8715 (m) cc_final: 0.8237 (t) REVERT: C 182 MET cc_start: 0.8070 (ttp) cc_final: 0.7830 (ttt) REVERT: C 438 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8844 (mm-30) REVERT: C 450 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8581 (mm-40) REVERT: D 282 ILE cc_start: 0.9204 (pt) cc_final: 0.8733 (pt) REVERT: D 435 LYS cc_start: 0.9469 (mmtp) cc_final: 0.9157 (mmtt) REVERT: D 450 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8257 (tm-30) REVERT: D 451 ASP cc_start: 0.8667 (m-30) cc_final: 0.8385 (m-30) REVERT: D 481 ILE cc_start: 0.8629 (mm) cc_final: 0.8419 (tt) REVERT: E 120 GLU cc_start: 0.8573 (pm20) cc_final: 0.8253 (pm20) REVERT: E 121 ARG cc_start: 0.8623 (ptt90) cc_final: 0.8305 (ptt-90) REVERT: E 275 PHE cc_start: 0.9184 (t80) cc_final: 0.8850 (t80) REVERT: E 296 TYR cc_start: 0.8197 (t80) cc_final: 0.7979 (t80) REVERT: E 321 ASP cc_start: 0.8641 (t0) cc_final: 0.7995 (t0) outliers start: 38 outliers final: 24 residues processed: 269 average time/residue: 0.0984 time to fit residues: 42.9116 Evaluate side-chains 263 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 481 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.081670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.065317 restraints weight = 88434.013| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 5.01 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16731 Z= 0.149 Angle : 0.594 12.870 22860 Z= 0.287 Chirality : 0.043 0.492 2602 Planarity : 0.003 0.040 2838 Dihedral : 5.647 59.884 2512 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.77 % Allowed : 19.58 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.39 (0.19), residues: 1985 helix: 2.29 (0.18), residues: 825 sheet: 0.53 (0.26), residues: 393 loop : -0.36 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 469 TYR 0.018 0.001 TYR B 296 PHE 0.009 0.001 PHE C 146 TRP 0.021 0.001 TRP C 330 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00347 (16706) covalent geometry : angle 0.56852 (22795) SS BOND : bond 0.00813 ( 10) SS BOND : angle 2.17173 ( 20) hydrogen bonds : bond 0.04738 ( 833) hydrogen bonds : angle 4.12416 ( 2616) link_BETA1-4 : bond 0.00348 ( 5) link_BETA1-4 : angle 1.89272 ( 15) link_NAG-ASN : bond 0.00363 ( 10) link_NAG-ASN : angle 4.24922 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8822 (t0) cc_final: 0.8332 (t0) REVERT: A 283 MET cc_start: 0.8333 (mmp) cc_final: 0.8095 (mmm) REVERT: B 347 ARG cc_start: 0.7980 (tmt-80) cc_final: 0.7535 (tmt-80) REVERT: B 471 CYS cc_start: 0.8710 (m) cc_final: 0.8289 (t) REVERT: C 283 MET cc_start: 0.8171 (mmm) cc_final: 0.7865 (mmm) REVERT: C 438 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8890 (mm-30) REVERT: C 450 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8608 (mm-40) REVERT: D 435 LYS cc_start: 0.9468 (mmtp) cc_final: 0.9028 (mttp) REVERT: D 450 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8239 (tm-30) REVERT: D 451 ASP cc_start: 0.8664 (m-30) cc_final: 0.8380 (m-30) REVERT: D 481 ILE cc_start: 0.8649 (mm) cc_final: 0.8434 (tt) REVERT: E 120 GLU cc_start: 0.8608 (pm20) cc_final: 0.8275 (pm20) REVERT: E 121 ARG cc_start: 0.8608 (ptt90) cc_final: 0.8270 (ptt-90) REVERT: E 321 ASP cc_start: 0.8640 (t0) cc_final: 0.8002 (t0) outliers start: 48 outliers final: 31 residues processed: 262 average time/residue: 0.1013 time to fit residues: 42.9913 Evaluate side-chains 271 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN D 319 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.064000 restraints weight = 91177.504| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 5.04 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16731 Z= 0.190 Angle : 0.628 18.574 22860 Z= 0.303 Chirality : 0.044 0.508 2602 Planarity : 0.004 0.039 2838 Dihedral : 5.404 47.731 2512 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.43 % Allowed : 20.15 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.37 (0.19), residues: 1985 helix: 2.25 (0.18), residues: 819 sheet: 0.49 (0.26), residues: 391 loop : -0.29 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 469 TYR 0.011 0.001 TYR E 296 PHE 0.011 0.001 PHE C 275 TRP 0.024 0.001 TRP C 330 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00442 (16706) covalent geometry : angle 0.60258 (22795) SS BOND : bond 0.00806 ( 10) SS BOND : angle 2.16472 ( 20) hydrogen bonds : bond 0.05030 ( 833) hydrogen bonds : angle 4.20710 ( 2616) link_BETA1-4 : bond 0.00307 ( 5) link_BETA1-4 : angle 1.87560 ( 15) link_NAG-ASN : bond 0.00408 ( 10) link_NAG-ASN : angle 4.40815 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8833 (t0) cc_final: 0.8273 (t0) REVERT: A 257 ASP cc_start: 0.9315 (m-30) cc_final: 0.8860 (m-30) REVERT: A 454 GLU cc_start: 0.8584 (pp20) cc_final: 0.8232 (pp20) REVERT: B 347 ARG cc_start: 0.7998 (tmt-80) cc_final: 0.7435 (tmt-80) REVERT: B 438 GLU cc_start: 0.9287 (mm-30) cc_final: 0.9077 (mm-30) REVERT: C 283 MET cc_start: 0.8488 (mmm) cc_final: 0.8158 (mmm) REVERT: C 450 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8576 (mm-40) REVERT: D 273 THR cc_start: 0.8864 (m) cc_final: 0.8566 (p) REVERT: D 327 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8330 (ttm) REVERT: D 450 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8204 (tm-30) REVERT: D 451 ASP cc_start: 0.8683 (m-30) cc_final: 0.8416 (m-30) REVERT: D 481 ILE cc_start: 0.8672 (mm) cc_final: 0.8459 (tt) REVERT: E 120 GLU cc_start: 0.8681 (pm20) cc_final: 0.8330 (pm20) REVERT: E 121 ARG cc_start: 0.8610 (ptt90) cc_final: 0.8202 (ptt-90) REVERT: E 321 ASP cc_start: 0.8673 (t0) cc_final: 0.8024 (t0) outliers start: 42 outliers final: 31 residues processed: 253 average time/residue: 0.0945 time to fit residues: 38.6901 Evaluate side-chains 263 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 18 optimal weight: 0.1980 chunk 111 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 chunk 36 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.066587 restraints weight = 96177.368| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 5.21 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16731 Z= 0.111 Angle : 0.571 10.594 22860 Z= 0.276 Chirality : 0.042 0.500 2602 Planarity : 0.003 0.038 2838 Dihedral : 4.971 38.969 2507 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.69 % Allowed : 20.94 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.48 (0.19), residues: 1985 helix: 2.44 (0.18), residues: 807 sheet: 0.55 (0.26), residues: 411 loop : -0.34 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 469 TYR 0.007 0.001 TYR D 296 PHE 0.008 0.001 PHE D 222 TRP 0.025 0.001 TRP C 330 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00253 (16706) covalent geometry : angle 0.54547 (22795) SS BOND : bond 0.00803 ( 10) SS BOND : angle 2.19238 ( 20) hydrogen bonds : bond 0.04482 ( 833) hydrogen bonds : angle 3.95547 ( 2616) link_BETA1-4 : bond 0.00458 ( 5) link_BETA1-4 : angle 1.74640 ( 15) link_NAG-ASN : bond 0.00405 ( 10) link_NAG-ASN : angle 4.18643 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8790 (t0) cc_final: 0.8310 (t0) REVERT: A 257 ASP cc_start: 0.9309 (m-30) cc_final: 0.8864 (m-30) REVERT: A 276 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8984 (tmm) REVERT: A 283 MET cc_start: 0.8166 (mmp) cc_final: 0.7940 (mmm) REVERT: B 197 ASP cc_start: 0.8245 (t0) cc_final: 0.7979 (t0) REVERT: B 347 ARG cc_start: 0.7995 (tmt-80) cc_final: 0.7397 (tmt-80) REVERT: B 438 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9050 (mm-30) REVERT: B 471 CYS cc_start: 0.8654 (m) cc_final: 0.8180 (t) REVERT: C 283 MET cc_start: 0.8502 (mmm) cc_final: 0.8240 (mmm) REVERT: C 450 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8555 (mm-40) REVERT: D 435 LYS cc_start: 0.9374 (mmtp) cc_final: 0.9155 (mmtt) REVERT: D 450 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8142 (tm-30) REVERT: D 451 ASP cc_start: 0.8679 (m-30) cc_final: 0.8359 (m-30) REVERT: D 471 CYS cc_start: 0.8564 (m) cc_final: 0.8207 (m) REVERT: D 481 ILE cc_start: 0.8676 (mm) cc_final: 0.8463 (tt) REVERT: E 120 GLU cc_start: 0.8641 (pm20) cc_final: 0.8274 (pm20) REVERT: E 121 ARG cc_start: 0.8620 (ptt90) cc_final: 0.8199 (ptt-90) REVERT: E 321 ASP cc_start: 0.8660 (t0) cc_final: 0.8002 (t0) outliers start: 29 outliers final: 19 residues processed: 264 average time/residue: 0.1012 time to fit residues: 43.1734 Evaluate side-chains 260 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 481 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 183 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.066848 restraints weight = 68946.180| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.40 r_work: 0.2809 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16731 Z= 0.117 Angle : 0.563 9.908 22860 Z= 0.275 Chirality : 0.042 0.490 2602 Planarity : 0.003 0.037 2838 Dihedral : 4.870 37.292 2507 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.35 % Allowed : 21.61 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.57 (0.19), residues: 1985 helix: 2.48 (0.18), residues: 807 sheet: 0.66 (0.25), residues: 417 loop : -0.29 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 469 TYR 0.023 0.001 TYR B 151 PHE 0.007 0.001 PHE C 275 TRP 0.020 0.001 TRP C 330 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00271 (16706) covalent geometry : angle 0.53803 (22795) SS BOND : bond 0.00813 ( 10) SS BOND : angle 2.18098 ( 20) hydrogen bonds : bond 0.04400 ( 833) hydrogen bonds : angle 3.91703 ( 2616) link_BETA1-4 : bond 0.00412 ( 5) link_BETA1-4 : angle 1.78859 ( 15) link_NAG-ASN : bond 0.00346 ( 10) link_NAG-ASN : angle 4.07057 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8944 (t0) cc_final: 0.8540 (t0) REVERT: A 257 ASP cc_start: 0.9362 (m-30) cc_final: 0.8948 (m-30) REVERT: A 283 MET cc_start: 0.8174 (mmp) cc_final: 0.7916 (mmm) REVERT: B 197 ASP cc_start: 0.8437 (t0) cc_final: 0.8175 (t0) REVERT: B 438 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9194 (mm-30) REVERT: B 471 CYS cc_start: 0.8769 (m) cc_final: 0.8398 (t) REVERT: C 283 MET cc_start: 0.8693 (mmm) cc_final: 0.8380 (mmt) REVERT: C 450 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8670 (mm-40) REVERT: D 327 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8219 (ttm) REVERT: D 450 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8283 (tm-30) REVERT: D 471 CYS cc_start: 0.8803 (m) cc_final: 0.8474 (m) REVERT: D 481 ILE cc_start: 0.8751 (mm) cc_final: 0.8506 (tt) REVERT: E 120 GLU cc_start: 0.8932 (pm20) cc_final: 0.8575 (pm20) REVERT: E 121 ARG cc_start: 0.8808 (ptt90) cc_final: 0.8400 (ptt-90) REVERT: E 321 ASP cc_start: 0.8880 (t0) cc_final: 0.8201 (t0) outliers start: 22 outliers final: 17 residues processed: 254 average time/residue: 0.0937 time to fit residues: 38.6534 Evaluate side-chains 259 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.065891 restraints weight = 95429.078| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 5.18 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16731 Z= 0.126 Angle : 0.576 11.178 22860 Z= 0.280 Chirality : 0.042 0.492 2602 Planarity : 0.003 0.037 2838 Dihedral : 4.812 35.817 2507 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.75 % Allowed : 21.44 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.58 (0.19), residues: 1985 helix: 2.46 (0.18), residues: 807 sheet: 0.68 (0.26), residues: 417 loop : -0.25 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 469 TYR 0.007 0.001 TYR D 296 PHE 0.007 0.001 PHE C 275 TRP 0.028 0.001 TRP C 330 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00293 (16706) covalent geometry : angle 0.55164 (22795) SS BOND : bond 0.00809 ( 10) SS BOND : angle 2.18192 ( 20) hydrogen bonds : bond 0.04422 ( 833) hydrogen bonds : angle 3.92678 ( 2616) link_BETA1-4 : bond 0.00377 ( 5) link_BETA1-4 : angle 1.77327 ( 15) link_NAG-ASN : bond 0.00336 ( 10) link_NAG-ASN : angle 4.08496 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8821 (t0) cc_final: 0.8348 (t0) REVERT: A 257 ASP cc_start: 0.9331 (m-30) cc_final: 0.8907 (m-30) REVERT: B 197 ASP cc_start: 0.8277 (t0) cc_final: 0.8001 (t0) REVERT: B 347 ARG cc_start: 0.8212 (tmt-80) cc_final: 0.7823 (tpt90) REVERT: B 438 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9045 (mm-30) REVERT: B 471 CYS cc_start: 0.8686 (m) cc_final: 0.8228 (t) REVERT: C 69 ASN cc_start: 0.9329 (m-40) cc_final: 0.8915 (m110) REVERT: C 283 MET cc_start: 0.8627 (mmm) cc_final: 0.8387 (mmm) REVERT: C 450 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8545 (mm-40) REVERT: D 327 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8364 (ttm) REVERT: D 450 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8102 (tm-30) REVERT: D 471 CYS cc_start: 0.8578 (m) cc_final: 0.8220 (m) REVERT: D 481 ILE cc_start: 0.8682 (mm) cc_final: 0.8468 (tt) REVERT: E 120 GLU cc_start: 0.8640 (pm20) cc_final: 0.8270 (pm20) REVERT: E 121 ARG cc_start: 0.8604 (ptt90) cc_final: 0.8169 (ptt-90) REVERT: E 321 ASP cc_start: 0.8671 (t0) cc_final: 0.8028 (t0) outliers start: 29 outliers final: 24 residues processed: 261 average time/residue: 0.0985 time to fit residues: 41.4318 Evaluate side-chains 267 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 195 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.081221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.065018 restraints weight = 108332.214| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 5.49 r_work: 0.2739 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16731 Z= 0.148 Angle : 0.591 10.136 22860 Z= 0.289 Chirality : 0.043 0.495 2602 Planarity : 0.003 0.038 2838 Dihedral : 4.816 34.449 2507 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.69 % Allowed : 21.61 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.58 (0.19), residues: 1985 helix: 2.42 (0.18), residues: 807 sheet: 0.69 (0.25), residues: 427 loop : -0.23 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.009 0.001 TYR D 296 PHE 0.008 0.001 PHE C 275 TRP 0.028 0.001 TRP C 330 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00347 (16706) covalent geometry : angle 0.56735 (22795) SS BOND : bond 0.00801 ( 10) SS BOND : angle 2.17757 ( 20) hydrogen bonds : bond 0.04590 ( 833) hydrogen bonds : angle 3.97733 ( 2616) link_BETA1-4 : bond 0.00310 ( 5) link_BETA1-4 : angle 1.76038 ( 15) link_NAG-ASN : bond 0.00339 ( 10) link_NAG-ASN : angle 4.14534 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8995 (t0) cc_final: 0.8538 (t0) REVERT: A 257 ASP cc_start: 0.9376 (m-30) cc_final: 0.8970 (m-30) REVERT: B 438 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9231 (mm-30) REVERT: B 471 CYS cc_start: 0.8825 (m) cc_final: 0.8431 (t) REVERT: C 69 ASN cc_start: 0.9429 (m-40) cc_final: 0.9046 (m110) REVERT: C 283 MET cc_start: 0.8795 (mmm) cc_final: 0.8527 (mmm) REVERT: C 450 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8685 (mm-40) REVERT: D 301 MET cc_start: 0.8362 (mmm) cc_final: 0.8157 (mmm) REVERT: D 327 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8279 (ttm) REVERT: D 450 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8329 (tm-30) REVERT: D 481 ILE cc_start: 0.8765 (mm) cc_final: 0.8515 (tt) REVERT: E 120 GLU cc_start: 0.8992 (pm20) cc_final: 0.8630 (pm20) REVERT: E 121 ARG cc_start: 0.8819 (ptt90) cc_final: 0.8391 (ptt-90) REVERT: E 321 ASP cc_start: 0.8907 (t0) cc_final: 0.8243 (t0) REVERT: E 327 MET cc_start: 0.7962 (ttm) cc_final: 0.7490 (ttt) outliers start: 28 outliers final: 23 residues processed: 254 average time/residue: 0.0898 time to fit residues: 37.3827 Evaluate side-chains 264 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 172 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 chunk 122 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 133 optimal weight: 0.1980 chunk 55 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.083007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.066822 restraints weight = 93961.233| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 5.16 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16731 Z= 0.112 Angle : 0.585 19.322 22860 Z= 0.282 Chirality : 0.042 0.485 2602 Planarity : 0.003 0.037 2838 Dihedral : 4.741 35.397 2507 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.41 % Allowed : 21.73 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.63 (0.19), residues: 1985 helix: 2.44 (0.18), residues: 807 sheet: 0.76 (0.26), residues: 417 loop : -0.20 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 448 TYR 0.008 0.000 TYR D 296 PHE 0.007 0.001 PHE A 297 TRP 0.028 0.001 TRP C 330 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00257 (16706) covalent geometry : angle 0.56262 (22795) SS BOND : bond 0.00811 ( 10) SS BOND : angle 2.19689 ( 20) hydrogen bonds : bond 0.04283 ( 833) hydrogen bonds : angle 3.89393 ( 2616) link_BETA1-4 : bond 0.00416 ( 5) link_BETA1-4 : angle 1.67582 ( 15) link_NAG-ASN : bond 0.00381 ( 10) link_NAG-ASN : angle 3.98368 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8819 (t0) cc_final: 0.8361 (t0) REVERT: A 257 ASP cc_start: 0.9331 (m-30) cc_final: 0.8926 (m-30) REVERT: A 283 MET cc_start: 0.8109 (mmp) cc_final: 0.7873 (mmm) REVERT: B 295 GLN cc_start: 0.8304 (mt0) cc_final: 0.8098 (mt0) REVERT: B 471 CYS cc_start: 0.8587 (m) cc_final: 0.8175 (t) REVERT: C 69 ASN cc_start: 0.9326 (m-40) cc_final: 0.8907 (m110) REVERT: C 275 PHE cc_start: 0.8503 (t80) cc_final: 0.8070 (t80) REVERT: D 301 MET cc_start: 0.8105 (mmm) cc_final: 0.7867 (mmm) REVERT: D 327 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8361 (ttm) REVERT: D 450 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8152 (tm-30) REVERT: D 471 CYS cc_start: 0.8554 (m) cc_final: 0.8195 (m) REVERT: E 120 GLU cc_start: 0.8635 (pm20) cc_final: 0.8260 (pm20) REVERT: E 121 ARG cc_start: 0.8599 (ptt90) cc_final: 0.8155 (ptt-90) REVERT: E 321 ASP cc_start: 0.8680 (t0) cc_final: 0.8000 (t0) REVERT: E 327 MET cc_start: 0.8030 (ttm) cc_final: 0.7612 (ttt) outliers start: 23 outliers final: 21 residues processed: 264 average time/residue: 0.0922 time to fit residues: 39.5592 Evaluate side-chains 267 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 17 optimal weight: 0.0020 chunk 68 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.083226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067673 restraints weight = 63005.256| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.22 r_work: 0.2815 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16731 Z= 0.115 Angle : 0.589 16.919 22860 Z= 0.287 Chirality : 0.042 0.480 2602 Planarity : 0.003 0.036 2838 Dihedral : 4.692 34.584 2507 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.24 % Allowed : 22.35 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 are not related in a simple way. whole: 1.64 (0.19), residues: 1985 helix: 2.43 (0.18), residues: 807 sheet: 0.81 (0.26), residues: 417 loop : -0.20 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.012 0.001 TYR E 217 PHE 0.007 0.001 PHE A 297 TRP 0.028 0.001 TRP C 330 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00268 (16706) covalent geometry : angle 0.56748 (22795) SS BOND : bond 0.00818 ( 10) SS BOND : angle 2.19465 ( 20) hydrogen bonds : bond 0.04229 ( 833) hydrogen bonds : angle 3.90908 ( 2616) link_BETA1-4 : bond 0.00391 ( 5) link_BETA1-4 : angle 1.71974 ( 15) link_NAG-ASN : bond 0.00339 ( 10) link_NAG-ASN : angle 3.91455 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2851.96 seconds wall clock time: 49 minutes 45.06 seconds (2985.06 seconds total)