Starting phenix.real_space_refine on Thu Feb 5 09:14:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lhd_63094/02_2026/9lhd_63094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lhd_63094/02_2026/9lhd_63094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lhd_63094/02_2026/9lhd_63094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lhd_63094/02_2026/9lhd_63094.map" model { file = "/net/cci-nas-00/data/ceres_data/9lhd_63094/02_2026/9lhd_63094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lhd_63094/02_2026/9lhd_63094.cif" } resolution = 3.24 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= 0.070 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 10477 2.51 5 N 2585 2.21 5 O 2936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s 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: 16113 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3178 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3171 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 400, 3171 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3249 Chain: "B" Number of atoms: 3172 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3165 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Conformer: "B" Number of residues, atoms: 400, 3165 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 bond proxies already assigned to first conformer: 3242 Chain: "C" Number of atoms: 3178 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3171 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 400, 3171 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3249 Chain: "D" Number of atoms: 3184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3177 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 400, 3177 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3255 Chain: "E" Number of atoms: 3178 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3171 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 400, 3171 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3249 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: 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: "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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.81, per 1000 atoms: 0.36 Number of scatterers: 16113 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 2936 8.00 N 2585 7.00 C 10477 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=2.04 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=2.07 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=2.05 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 601 " - " 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: 1.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 58 helices and 22 sheets defined 45.1% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.558A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 238 through 249 Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 260 through 281 removed outlier: 3.578A 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 337 through 343 Processing helix chain 'A' and resid 431 through 490 removed outlier: 4.210A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.778A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 262 through 283 removed outlier: 4.235A pdb=" N VAL B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 321 through 325 removed outlier: 4.100A pdb=" N GLY B 325 " --> pdb=" O PRO B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 338 through 344 Processing helix chain 'B' and resid 431 through 489 Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.777A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 260 through 281 removed outlier: 3.989A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 removed outlier: 3.813A pdb=" N SER C 299 " --> pdb=" O GLN C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 431 through 489 removed outlier: 3.834A pdb=" N LYS C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 502 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.767A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.521A pdb=" N LEU D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) 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 276 removed outlier: 3.942A pdb=" N LEU D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 281 Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 431 through 489 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.818A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 249 removed outlier: 4.535A pdb=" N ILE E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix removed outlier: 3.533A pdb=" N LEU E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 253 Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 260 through 283 removed outlier: 4.219A pdb=" N LEU E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 319 removed outlier: 3.534A pdb=" N PHE E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 337 through 344 removed outlier: 3.522A pdb=" N TRP E 341 " --> pdb=" O ASN E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 490 removed outlier: 4.424A pdb=" N ALA E 490 " --> pdb=" O ILE E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.783A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN A 79 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER A 58 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N SER A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER A 56 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N THR A 83 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N TYR A 54 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.685A 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: 3.510A pdb=" N LEU A 113 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.821A 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: 3.510A pdb=" N LEU A 113 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 55 removed outlier: 6.098A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 66 removed outlier: 7.512A pdb=" N LEU B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N TRP B 77 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.575A pdb=" N GLY B 169 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.907A 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: 3.575A pdb=" N GLY B 169 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.553A pdb=" N TRP C 82 " --> pdb=" O CYS C 138 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 79 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N THR C 83 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR C 52 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C 53 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.998A pdb=" N LEU C 60 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N TRP C 77 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE C 62 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 76 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 144 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.998A pdb=" N LEU C 60 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N TRP C 77 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE C 62 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.503A pdb=" N LEU C 113 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY C 169 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.503A pdb=" N LEU C 113 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY C 169 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 221 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 204 " --> pdb=" O THR C 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 102 removed outlier: 4.220A pdb=" N HIS D 137 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 59 through 66 removed outlier: 5.760A pdb=" N ILE D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN D 75 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 112 through 114 removed outlier: 3.727A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 114 removed outlier: 3.727A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR D 221 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 99 through 102 removed outlier: 4.120A pdb=" N HIS E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 99 through 102 removed outlier: 4.120A pdb=" N HIS E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 71 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N THR E 83 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 9.773A pdb=" N TYR E 54 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 112 through 114 removed outlier: 3.769A pdb=" N GLY E 169 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 112 through 114 removed outlier: 3.769A pdb=" N GLY E 169 " --> pdb=" O LEU E 113 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2550 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: 2.67 Time building geometry restraints manager: 1.36 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: 2560 1.32 - 1.45: 4664 1.45 - 1.58: 9161 1.58 - 1.72: 2 1.72 - 1.85: 170 Bond restraints: 16557 Sorted by residual: bond pdb=" C6 NCT A 601 " pdb=" C7 NCT A 601 " ideal model delta sigma weight residual 1.536 1.366 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" C6 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.620 -0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" C9 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.302 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C7 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C7 NAG E 601 " pdb=" N2 NAG E 601 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 16552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 22073 2.00 - 4.01: 415 4.01 - 6.01: 93 6.01 - 8.02: 18 8.02 - 10.02: 6 Bond angle restraints: 22605 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 109.38 119.40 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CG MET D 301 " pdb=" SD MET D 301 " pdb=" CE MET D 301 " ideal model delta sigma weight residual 100.90 108.01 -7.11 2.20e+00 2.07e-01 1.04e+01 angle pdb=" C SER D 271 " pdb=" N LEU D 272 " pdb=" CA LEU D 272 " ideal model delta sigma weight residual 120.68 115.31 5.37 1.70e+00 3.46e-01 9.98e+00 angle pdb=" C VAL E 333 " pdb=" N ILE E 334 " pdb=" CA ILE E 334 " ideal model delta sigma weight residual 122.97 119.97 3.00 9.80e-01 1.04e+00 9.34e+00 angle pdb=" CA LEU B 277 " pdb=" CB LEU B 277 " pdb=" CG LEU B 277 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.73e+00 ... (remaining 22600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 8687 18.13 - 36.25: 1034 36.25 - 54.38: 199 54.38 - 72.51: 32 72.51 - 90.64: 9 Dihedral angle restraints: 9961 sinusoidal: 4066 harmonic: 5895 Sorted by residual: dihedral pdb=" CB CYS B 150 " pdb=" SG CYS B 150 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 38.29 54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CA CYS B 212 " pdb=" C CYS B 212 " pdb=" N CYS B 213 " pdb=" CA CYS B 213 " ideal model delta harmonic sigma weight residual -180.00 -152.28 -27.72 0 5.00e+00 4.00e-02 3.07e+01 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 47.33 45.67 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 9958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1962 0.047 - 0.094: 502 0.094 - 0.141: 117 0.141 - 0.187: 19 0.187 - 0.234: 1 Chirality restraints: 2601 Sorted by residual: chirality pdb=" CG LEU D 272 " pdb=" CB LEU D 272 " pdb=" CD1 LEU D 272 " pdb=" CD2 LEU D 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.18 2.00e-01 2.50e+01 8.28e-01 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 -2.22 -0.18 2.00e-01 2.50e+01 8.22e-01 ... (remaining 2598 not shown) Planarity restraints: 2831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 94 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO C 95 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 283 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO E 284 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 284 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 284 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 176 " -0.016 2.00e-02 2.50e+03 1.08e-02 2.93e+00 pdb=" CG TRP C 176 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP C 176 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C 176 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 176 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 176 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 176 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 176 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 176 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 176 " -0.001 2.00e-02 2.50e+03 ... (remaining 2828 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1586 2.74 - 3.28: 15603 3.28 - 3.82: 26759 3.82 - 4.36: 29487 4.36 - 4.90: 53064 Nonbonded interactions: 126499 Sorted by model distance: nonbonded pdb=" OG SER C 206 " pdb=" OD1 ASP C 219 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN B 46 " pdb=" OG SER B 48 " model vdw 2.212 3.040 nonbonded pdb=" O VAL B 251 " pdb=" NZ LYS B 261 " model vdw 2.218 3.120 nonbonded pdb=" N GLU C 184 " pdb=" OE1 GLU C 184 " model vdw 2.220 3.120 nonbonded pdb=" NZ LYS E 167 " pdb=" OD2 ASP E 219 " model vdw 2.237 3.120 ... (remaining 126494 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 341 or (resid 342 and \ (name N or name CA or name C or name O or name CB )) or resid 343 through 502)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 502)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 341 or (resid 342 and \ (name N or name CA or name C or name O or name CB )) or resid 343 through 502)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 341 or (resid 342 and \ (name N or name CA or name C or name O or name CB )) or resid 343 through 346 or \ (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 8 through 502)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 341 or (resid 342 and \ (name N or name CA or name C or name O or name CB )) or resid 343 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=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.300 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 16582 Z= 0.388 Angle : 0.727 10.021 22670 Z= 0.337 Chirality : 0.044 0.234 2601 Planarity : 0.004 0.052 2821 Dihedral : 15.528 90.637 6121 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.06 % Allowed : 22.40 % Favored : 77.54 % 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: 0.40 (0.19), residues: 1985 helix: 1.80 (0.18), residues: 796 sheet: -0.55 (0.26), residues: 413 loop : -0.86 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 121 TYR 0.016 0.001 TYR D 442 PHE 0.027 0.001 PHE D 275 TRP 0.029 0.001 TRP C 176 HIS 0.006 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00819 (16557) covalent geometry : angle 0.71524 (22605) SS BOND : bond 0.01392 ( 10) SS BOND : angle 2.80185 ( 20) hydrogen bonds : bond 0.14481 ( 825) hydrogen bonds : angle 5.62784 ( 2550) link_BETA1-4 : bond 0.00200 ( 5) link_BETA1-4 : angle 1.05198 ( 15) link_NAG-ASN : bond 0.00456 ( 10) link_NAG-ASN : angle 2.88778 ( 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 268 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.8941 (mm) cc_final: 0.8582 (mm) REVERT: B 236 ASN cc_start: 0.9161 (m-40) cc_final: 0.8937 (m-40) REVERT: B 450 GLN cc_start: 0.9471 (mt0) cc_final: 0.8855 (mt0) REVERT: B 454 GLU cc_start: 0.9171 (tt0) cc_final: 0.8882 (mt-10) REVERT: C 243 LEU cc_start: 0.8661 (tt) cc_final: 0.8088 (mt) REVERT: C 450 GLN cc_start: 0.9047 (mt0) cc_final: 0.8786 (mt0) REVERT: D 488 MET cc_start: 0.8423 (tpp) cc_final: 0.8218 (mmt) REVERT: E 476 SER cc_start: 0.9330 (t) cc_final: 0.8841 (p) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.0995 time to fit residues: 41.8423 Evaluate side-chains 215 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN C 492 ASN E 137 HIS A Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.082189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.067785 restraints weight = 86631.188| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.62 r_work: 0.2741 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16582 Z= 0.142 Angle : 0.624 9.544 22670 Z= 0.304 Chirality : 0.042 0.385 2601 Planarity : 0.004 0.045 2821 Dihedral : 6.215 60.195 2489 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.26 % Allowed : 23.03 % Favored : 75.71 % 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: 0.56 (0.19), residues: 1985 helix: 1.96 (0.18), residues: 800 sheet: -0.25 (0.26), residues: 425 loop : -0.96 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 332 TYR 0.021 0.001 TYR D 296 PHE 0.014 0.001 PHE A 478 TRP 0.040 0.001 TRP B 176 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00314 (16557) covalent geometry : angle 0.60118 (22605) SS BOND : bond 0.00918 ( 10) SS BOND : angle 2.90647 ( 20) hydrogen bonds : bond 0.05452 ( 825) hydrogen bonds : angle 4.46800 ( 2550) link_BETA1-4 : bond 0.00584 ( 5) link_BETA1-4 : angle 1.54098 ( 15) link_NAG-ASN : bond 0.00423 ( 10) link_NAG-ASN : angle 3.89563 ( 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 247 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 PHE cc_start: 0.8779 (m-80) cc_final: 0.8377 (m-80) REVERT: B 236 ASN cc_start: 0.9099 (m-40) cc_final: 0.8894 (m110) REVERT: B 296 TYR cc_start: 0.8841 (t80) cc_final: 0.8518 (t80) REVERT: B 450 GLN cc_start: 0.9506 (mt0) cc_final: 0.8979 (mt0) REVERT: B 454 GLU cc_start: 0.9403 (tt0) cc_final: 0.9078 (mt-10) REVERT: C 176 TRP cc_start: 0.7459 (m100) cc_final: 0.7137 (m100) REVERT: C 239 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8396 (mt) REVERT: C 243 LEU cc_start: 0.8552 (tt) cc_final: 0.7970 (mt) REVERT: C 275 PHE cc_start: 0.8983 (t80) cc_final: 0.8646 (t80) REVERT: C 471 CYS cc_start: 0.9141 (m) cc_final: 0.8763 (t) REVERT: D 182 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8895 (tmm) REVERT: D 488 MET cc_start: 0.8516 (tpp) cc_final: 0.8314 (mmt) REVERT: E 245 SER cc_start: 0.9341 (t) cc_final: 0.9044 (p) REVERT: E 476 SER cc_start: 0.9218 (t) cc_final: 0.8800 (p) outliers start: 22 outliers final: 12 residues processed: 235 average time/residue: 0.0963 time to fit residues: 37.6229 Evaluate side-chains 231 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 459 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 90 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.080566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.066142 restraints weight = 82224.637| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 4.49 r_work: 0.2707 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16582 Z= 0.199 Angle : 0.628 8.946 22670 Z= 0.307 Chirality : 0.042 0.392 2601 Planarity : 0.004 0.043 2821 Dihedral : 5.708 50.600 2489 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.60 % Allowed : 22.69 % Favored : 75.71 % 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: 0.61 (0.19), residues: 1985 helix: 1.93 (0.18), residues: 804 sheet: 0.01 (0.26), residues: 405 loop : -1.00 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 208 TYR 0.018 0.001 TYR D 296 PHE 0.024 0.001 PHE D 275 TRP 0.041 0.001 TRP B 176 HIS 0.005 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00458 (16557) covalent geometry : angle 0.60522 (22605) SS BOND : bond 0.00869 ( 10) SS BOND : angle 2.85709 ( 20) hydrogen bonds : bond 0.05587 ( 825) hydrogen bonds : angle 4.39678 ( 2550) link_BETA1-4 : bond 0.00346 ( 5) link_BETA1-4 : angle 1.49181 ( 15) link_NAG-ASN : bond 0.00364 ( 10) link_NAG-ASN : angle 3.98170 ( 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 248 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 PHE cc_start: 0.8886 (m-80) cc_final: 0.8469 (m-80) REVERT: A 480 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9122 (mp) REVERT: B 120 GLU cc_start: 0.8573 (pp20) cc_final: 0.8168 (pp20) REVERT: B 450 GLN cc_start: 0.9531 (mt0) cc_final: 0.9051 (mt0) REVERT: B 454 GLU cc_start: 0.9387 (tt0) cc_final: 0.9061 (mt-10) REVERT: C 176 TRP cc_start: 0.7708 (m100) cc_final: 0.7213 (m100) REVERT: C 243 LEU cc_start: 0.8586 (tt) cc_final: 0.8022 (mt) REVERT: C 275 PHE cc_start: 0.9021 (t80) cc_final: 0.8619 (t80) REVERT: C 471 CYS cc_start: 0.9135 (m) cc_final: 0.8769 (t) REVERT: D 97 VAL cc_start: 0.9687 (OUTLIER) cc_final: 0.9396 (m) REVERT: D 182 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8975 (tmm) REVERT: E 454 GLU cc_start: 0.8862 (pp20) cc_final: 0.8576 (pp20) REVERT: E 476 SER cc_start: 0.9202 (t) cc_final: 0.8796 (p) outliers start: 28 outliers final: 16 residues processed: 230 average time/residue: 0.0931 time to fit residues: 35.3794 Evaluate side-chains 227 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 459 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.067690 restraints weight = 54280.792| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.59 r_work: 0.2763 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16582 Z= 0.152 Angle : 0.593 9.141 22670 Z= 0.290 Chirality : 0.041 0.408 2601 Planarity : 0.003 0.044 2821 Dihedral : 5.145 42.680 2489 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.54 % Allowed : 22.80 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.69 (0.19), residues: 1985 helix: 1.98 (0.18), residues: 808 sheet: 0.10 (0.26), residues: 405 loop : -0.99 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 208 TYR 0.018 0.001 TYR D 296 PHE 0.025 0.001 PHE D 275 TRP 0.026 0.001 TRP B 176 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00344 (16557) covalent geometry : angle 0.57018 (22605) SS BOND : bond 0.00967 ( 10) SS BOND : angle 2.77603 ( 20) hydrogen bonds : bond 0.05291 ( 825) hydrogen bonds : angle 4.22019 ( 2550) link_BETA1-4 : bond 0.00473 ( 5) link_BETA1-4 : angle 1.29153 ( 15) link_NAG-ASN : bond 0.00316 ( 10) link_NAG-ASN : angle 3.87069 ( 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 245 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ILE cc_start: 0.9208 (mp) cc_final: 0.8928 (mp) REVERT: A 475 PHE cc_start: 0.8898 (m-80) cc_final: 0.8491 (m-80) REVERT: A 480 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9070 (mp) REVERT: B 450 GLN cc_start: 0.9526 (mt0) cc_final: 0.8941 (mt0) REVERT: B 454 GLU cc_start: 0.9349 (tt0) cc_final: 0.9018 (mt-10) REVERT: C 239 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8452 (mt) REVERT: C 243 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7994 (mt) REVERT: C 275 PHE cc_start: 0.9024 (t80) cc_final: 0.8627 (t80) REVERT: C 471 CYS cc_start: 0.9097 (m) cc_final: 0.8755 (t) REVERT: D 97 VAL cc_start: 0.9663 (OUTLIER) cc_final: 0.9379 (m) REVERT: D 438 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8519 (mm-30) REVERT: E 454 GLU cc_start: 0.8834 (pp20) cc_final: 0.8530 (pp20) REVERT: E 476 SER cc_start: 0.9196 (t) cc_final: 0.8783 (p) outliers start: 27 outliers final: 16 residues processed: 229 average time/residue: 0.0982 time to fit residues: 37.3764 Evaluate side-chains 231 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 459 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 20 optimal weight: 9.9990 chunk 178 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3180 r_free = 0.3180 target = 0.081560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.066622 restraints weight = 106442.901| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 5.11 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16582 Z= 0.139 Angle : 0.586 9.209 22670 Z= 0.285 Chirality : 0.041 0.411 2601 Planarity : 0.003 0.042 2821 Dihedral : 4.924 33.263 2489 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.94 % Allowed : 22.40 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.79 (0.19), residues: 1985 helix: 2.07 (0.18), residues: 808 sheet: 0.19 (0.26), residues: 405 loop : -0.98 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 208 TYR 0.019 0.001 TYR D 296 PHE 0.028 0.001 PHE D 275 TRP 0.022 0.001 TRP B 176 HIS 0.003 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00314 (16557) covalent geometry : angle 0.56297 (22605) SS BOND : bond 0.00896 ( 10) SS BOND : angle 2.88196 ( 20) hydrogen bonds : bond 0.05136 ( 825) hydrogen bonds : angle 4.12551 ( 2550) link_BETA1-4 : bond 0.00426 ( 5) link_BETA1-4 : angle 1.25771 ( 15) link_NAG-ASN : bond 0.00317 ( 10) link_NAG-ASN : angle 3.76243 ( 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 254 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 PHE cc_start: 0.8792 (m-80) cc_final: 0.8404 (m-80) REVERT: A 480 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9086 (mp) REVERT: B 450 GLN cc_start: 0.9463 (mt0) cc_final: 0.8845 (mt0) REVERT: B 454 GLU cc_start: 0.9168 (tt0) cc_final: 0.8835 (mt-10) REVERT: C 239 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8366 (mt) REVERT: C 243 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7979 (mt) REVERT: C 275 PHE cc_start: 0.9058 (t80) cc_final: 0.8692 (t80) REVERT: C 471 CYS cc_start: 0.8807 (m) cc_final: 0.8538 (t) REVERT: D 97 VAL cc_start: 0.9614 (OUTLIER) cc_final: 0.9312 (m) REVERT: E 147 LYS cc_start: 0.9346 (mtpt) cc_final: 0.9096 (mtpp) REVERT: E 454 GLU cc_start: 0.8696 (pp20) cc_final: 0.8388 (pp20) REVERT: E 476 SER cc_start: 0.9158 (t) cc_final: 0.8641 (p) outliers start: 34 outliers final: 21 residues processed: 237 average time/residue: 0.1002 time to fit residues: 39.4048 Evaluate side-chains 241 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 459 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.080232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.065798 restraints weight = 83898.877| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 4.54 r_work: 0.2702 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16582 Z= 0.186 Angle : 0.611 9.489 22670 Z= 0.299 Chirality : 0.042 0.425 2601 Planarity : 0.003 0.041 2821 Dihedral : 4.954 31.825 2489 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.00 % Allowed : 22.34 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.79 (0.19), residues: 1985 helix: 2.01 (0.18), residues: 808 sheet: 0.25 (0.26), residues: 413 loop : -0.95 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 208 TYR 0.016 0.001 TYR D 296 PHE 0.024 0.001 PHE D 275 TRP 0.022 0.001 TRP B 176 HIS 0.005 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00429 (16557) covalent geometry : angle 0.58823 (22605) SS BOND : bond 0.01031 ( 10) SS BOND : angle 2.80280 ( 20) hydrogen bonds : bond 0.05392 ( 825) hydrogen bonds : angle 4.21227 ( 2550) link_BETA1-4 : bond 0.00314 ( 5) link_BETA1-4 : angle 1.31088 ( 15) link_NAG-ASN : bond 0.00348 ( 10) link_NAG-ASN : angle 3.89940 ( 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 246 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7854 (t80) REVERT: A 475 PHE cc_start: 0.8900 (m-80) cc_final: 0.8449 (m-80) REVERT: A 480 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9125 (mp) REVERT: B 450 GLN cc_start: 0.9535 (mt0) cc_final: 0.8959 (mt0) REVERT: B 454 GLU cc_start: 0.9395 (tt0) cc_final: 0.9062 (mt-10) REVERT: C 160 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: C 239 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8485 (mt) REVERT: C 243 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7985 (mt) REVERT: C 275 PHE cc_start: 0.9010 (t80) cc_final: 0.8600 (t80) REVERT: C 471 CYS cc_start: 0.9141 (m) cc_final: 0.8816 (t) REVERT: D 97 VAL cc_start: 0.9655 (OUTLIER) cc_final: 0.9427 (m) REVERT: E 454 GLU cc_start: 0.8884 (pp20) cc_final: 0.8587 (pp20) REVERT: E 476 SER cc_start: 0.9201 (t) cc_final: 0.8788 (p) outliers start: 35 outliers final: 22 residues processed: 229 average time/residue: 0.0885 time to fit residues: 33.5747 Evaluate side-chains 240 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 459 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 151 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.081964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.067280 restraints weight = 94188.712| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 4.83 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16582 Z= 0.124 Angle : 0.574 9.464 22670 Z= 0.281 Chirality : 0.041 0.422 2601 Planarity : 0.003 0.041 2821 Dihedral : 4.759 31.382 2489 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.77 % Allowed : 22.80 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.92 (0.19), residues: 1985 helix: 2.14 (0.18), residues: 808 sheet: 0.34 (0.26), residues: 413 loop : -0.92 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 208 TYR 0.017 0.001 TYR D 296 PHE 0.025 0.001 PHE D 275 TRP 0.059 0.001 TRP B 176 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00276 (16557) covalent geometry : angle 0.55217 (22605) SS BOND : bond 0.00940 ( 10) SS BOND : angle 2.86745 ( 20) hydrogen bonds : bond 0.04980 ( 825) hydrogen bonds : angle 4.00662 ( 2550) link_BETA1-4 : bond 0.00475 ( 5) link_BETA1-4 : angle 1.14031 ( 15) link_NAG-ASN : bond 0.00329 ( 10) link_NAG-ASN : angle 3.66186 ( 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 255 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8784 (t70) cc_final: 0.8510 (t70) REVERT: A 275 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7888 (t80) REVERT: A 475 PHE cc_start: 0.8772 (m-80) cc_final: 0.8352 (m-80) REVERT: A 480 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9093 (mp) REVERT: B 450 GLN cc_start: 0.9463 (mt0) cc_final: 0.8829 (mt0) REVERT: B 454 GLU cc_start: 0.9149 (tt0) cc_final: 0.8819 (mt-10) REVERT: C 160 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8094 (t0) REVERT: C 239 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8350 (mt) REVERT: C 243 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7916 (mt) REVERT: C 275 PHE cc_start: 0.9053 (t80) cc_final: 0.8697 (t80) REVERT: C 471 CYS cc_start: 0.8770 (m) cc_final: 0.8526 (t) REVERT: D 97 VAL cc_start: 0.9571 (OUTLIER) cc_final: 0.9331 (m) REVERT: D 182 MET cc_start: 0.8627 (tmm) cc_final: 0.8126 (tmm) REVERT: E 147 LYS cc_start: 0.9331 (mtpt) cc_final: 0.9093 (mtpp) REVERT: E 454 GLU cc_start: 0.8718 (pp20) cc_final: 0.8446 (pp20) REVERT: E 476 SER cc_start: 0.9179 (t) cc_final: 0.8636 (p) outliers start: 31 outliers final: 23 residues processed: 239 average time/residue: 0.0897 time to fit residues: 35.3766 Evaluate side-chains 244 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 459 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 57 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 88 optimal weight: 0.0370 chunk 163 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 146 optimal weight: 0.0870 chunk 158 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.070310 restraints weight = 103450.596| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 5.28 r_work: 0.2780 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 16582 Z= 0.109 Angle : 0.564 9.412 22670 Z= 0.275 Chirality : 0.040 0.418 2601 Planarity : 0.003 0.041 2821 Dihedral : 4.461 31.681 2489 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.66 % Allowed : 22.97 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.12 (0.19), residues: 1985 helix: 2.29 (0.18), residues: 808 sheet: 0.50 (0.26), residues: 415 loop : -0.83 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 121 TYR 0.019 0.001 TYR C 151 PHE 0.026 0.001 PHE D 275 TRP 0.035 0.001 TRP B 176 HIS 0.002 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00231 (16557) covalent geometry : angle 0.54442 (22605) SS BOND : bond 0.00929 ( 10) SS BOND : angle 2.88470 ( 20) hydrogen bonds : bond 0.04349 ( 825) hydrogen bonds : angle 3.78971 ( 2550) link_BETA1-4 : bond 0.00547 ( 5) link_BETA1-4 : angle 1.13199 ( 15) link_NAG-ASN : bond 0.00371 ( 10) link_NAG-ASN : angle 3.32245 ( 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 273 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8826 (t70) cc_final: 0.8601 (t70) REVERT: A 275 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7786 (t80) REVERT: A 475 PHE cc_start: 0.8924 (m-80) cc_final: 0.8537 (m-80) REVERT: B 296 TYR cc_start: 0.8858 (t80) cc_final: 0.8551 (t80) REVERT: B 450 GLN cc_start: 0.9493 (mt0) cc_final: 0.8936 (mt0) REVERT: B 454 GLU cc_start: 0.9400 (tt0) cc_final: 0.9045 (mt-10) REVERT: C 160 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8387 (t0) REVERT: C 239 ILE cc_start: 0.8722 (mt) cc_final: 0.8429 (mt) REVERT: C 243 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7934 (mt) REVERT: C 471 CYS cc_start: 0.9123 (m) cc_final: 0.8817 (m) REVERT: D 182 MET cc_start: 0.9144 (tmm) cc_final: 0.8880 (tmm) REVERT: D 438 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8701 (mm-30) REVERT: E 147 LYS cc_start: 0.9481 (mtpt) cc_final: 0.9272 (mtpp) REVERT: E 454 GLU cc_start: 0.8823 (pp20) cc_final: 0.8560 (pp20) REVERT: E 476 SER cc_start: 0.9219 (t) cc_final: 0.8765 (p) outliers start: 29 outliers final: 16 residues processed: 260 average time/residue: 0.1005 time to fit residues: 42.9294 Evaluate side-chains 252 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 154 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.079867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.065605 restraints weight = 84904.984| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 4.51 r_work: 0.2695 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16582 Z= 0.231 Angle : 0.650 9.668 22670 Z= 0.320 Chirality : 0.043 0.443 2601 Planarity : 0.004 0.039 2821 Dihedral : 4.842 35.460 2489 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.43 % Allowed : 23.71 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.94 (0.19), residues: 1985 helix: 2.09 (0.18), residues: 808 sheet: 0.35 (0.26), residues: 423 loop : -0.83 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 228 TYR 0.019 0.002 TYR A 232 PHE 0.020 0.001 PHE D 275 TRP 0.047 0.002 TRP D 176 HIS 0.006 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00530 (16557) covalent geometry : angle 0.62957 (22605) SS BOND : bond 0.00946 ( 10) SS BOND : angle 2.82333 ( 20) hydrogen bonds : bond 0.05420 ( 825) hydrogen bonds : angle 4.18537 ( 2550) link_BETA1-4 : bond 0.00331 ( 5) link_BETA1-4 : angle 1.42254 ( 15) link_NAG-ASN : bond 0.00436 ( 10) link_NAG-ASN : angle 3.83952 ( 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 235 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7934 (t80) REVERT: A 475 PHE cc_start: 0.8886 (m-80) cc_final: 0.8431 (m-80) REVERT: B 450 GLN cc_start: 0.9521 (mt0) cc_final: 0.9014 (mt0) REVERT: B 454 GLU cc_start: 0.9389 (tt0) cc_final: 0.9057 (mt-10) REVERT: C 160 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8453 (m-30) REVERT: C 243 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7942 (mt) REVERT: C 275 PHE cc_start: 0.9008 (t80) cc_final: 0.8618 (t80) REVERT: D 182 MET cc_start: 0.9110 (tmm) cc_final: 0.8635 (tmm) REVERT: E 176 TRP cc_start: 0.8765 (m100) cc_final: 0.8216 (m100) REVERT: E 454 GLU cc_start: 0.8856 (pp20) cc_final: 0.8601 (pp20) REVERT: E 476 SER cc_start: 0.9228 (t) cc_final: 0.8759 (p) outliers start: 25 outliers final: 19 residues processed: 225 average time/residue: 0.1050 time to fit residues: 38.5939 Evaluate side-chains 230 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 459 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 90 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 76 optimal weight: 0.0370 chunk 138 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.080953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.066865 restraints weight = 74503.704| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.26 r_work: 0.2726 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16582 Z= 0.157 Angle : 0.612 9.674 22670 Z= 0.299 Chirality : 0.041 0.434 2601 Planarity : 0.003 0.042 2821 Dihedral : 4.775 33.598 2489 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.49 % Allowed : 23.60 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.00 (0.19), residues: 1985 helix: 2.11 (0.18), residues: 808 sheet: 0.39 (0.26), residues: 431 loop : -0.79 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 121 TYR 0.020 0.001 TYR D 296 PHE 0.030 0.001 PHE D 275 TRP 0.039 0.001 TRP B 176 HIS 0.004 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00364 (16557) covalent geometry : angle 0.58837 (22605) SS BOND : bond 0.00953 ( 10) SS BOND : angle 3.35199 ( 20) hydrogen bonds : bond 0.05174 ( 825) hydrogen bonds : angle 4.08579 ( 2550) link_BETA1-4 : bond 0.00381 ( 5) link_BETA1-4 : angle 1.17649 ( 15) link_NAG-ASN : bond 0.00298 ( 10) link_NAG-ASN : angle 3.70691 ( 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 235 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7907 (t80) REVERT: A 475 PHE cc_start: 0.8894 (m-80) cc_final: 0.8423 (m-80) REVERT: B 450 GLN cc_start: 0.9520 (mt0) cc_final: 0.8942 (mt0) REVERT: B 454 GLU cc_start: 0.9378 (tt0) cc_final: 0.9041 (mt-10) REVERT: C 243 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7935 (mt) REVERT: C 275 PHE cc_start: 0.9002 (t80) cc_final: 0.8632 (t80) REVERT: D 182 MET cc_start: 0.9118 (tmm) cc_final: 0.8847 (tmm) REVERT: E 454 GLU cc_start: 0.8839 (pp20) cc_final: 0.8575 (pp20) REVERT: E 476 SER cc_start: 0.9211 (t) cc_final: 0.8757 (p) outliers start: 26 outliers final: 20 residues processed: 224 average time/residue: 0.0928 time to fit residues: 34.0737 Evaluate side-chains 228 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 459 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 118 optimal weight: 0.0980 chunk 146 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 196 optimal weight: 0.0980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.082049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.067654 restraints weight = 83987.374| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 4.58 r_work: 0.2749 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16582 Z= 0.130 Angle : 0.597 9.484 22670 Z= 0.291 Chirality : 0.041 0.424 2601 Planarity : 0.003 0.041 2821 Dihedral : 4.649 32.795 2489 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.09 % Allowed : 24.06 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.08 (0.19), residues: 1985 helix: 2.20 (0.18), residues: 809 sheet: 0.43 (0.25), residues: 431 loop : -0.78 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 121 TYR 0.020 0.001 TYR D 296 PHE 0.030 0.001 PHE D 275 TRP 0.037 0.001 TRP B 176 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00298 (16557) covalent geometry : angle 0.57400 (22605) SS BOND : bond 0.00962 ( 10) SS BOND : angle 3.40885 ( 20) hydrogen bonds : bond 0.04901 ( 825) hydrogen bonds : angle 3.97140 ( 2550) link_BETA1-4 : bond 0.00462 ( 5) link_BETA1-4 : angle 1.13560 ( 15) link_NAG-ASN : bond 0.00302 ( 10) link_NAG-ASN : angle 3.54860 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3442.96 seconds wall clock time: 59 minutes 46.18 seconds (3586.18 seconds total)