Starting phenix.real_space_refine on Thu Feb 5 09:40:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lhc_63093/02_2026/9lhc_63093.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lhc_63093/02_2026/9lhc_63093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lhc_63093/02_2026/9lhc_63093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lhc_63093/02_2026/9lhc_63093.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lhc_63093/02_2026/9lhc_63093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lhc_63093/02_2026/9lhc_63093.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10527 2.51 5 N 2601 2.21 5 O 2947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 16190 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "B" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "C" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "D" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "E" Number of atoms: 3186 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3179 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 400, 3179 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 3257 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: 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.67, per 1000 atoms: 0.41 Number of scatterers: 16190 At special positions: 0 Unit cell: (90.9, 95.95, 168.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 2947 8.00 N 2601 7.00 C 10527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 602 " - " ASN A 46 " " NAG B 601 " - " ASN B 46 " " NAG C 602 " - " 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: 0.90 Conformation dependent library (CDL) restraints added in 941.3 milliseconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 44.0% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.573A 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 237 through 248 Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.806A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.732A pdb=" N TRP A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 489 Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.875A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 237 through 249 removed outlier: 3.783A pdb=" N CYS B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 261 through 283 removed outlier: 3.788A pdb=" N GLY B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 328 through 335 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.732A pdb=" N TRP B 341 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 489 removed outlier: 3.688A pdb=" N ILE B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.896A 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 232 through 237 Processing helix chain 'C' and resid 238 through 248 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 261 through 283 Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 431 through 490 removed outlier: 4.299A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 502 removed outlier: 3.587A pdb=" N ALA C 496 " --> pdb=" O ASN C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.662A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 237 Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.636A pdb=" N CYS D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 removed outlier: 4.209A pdb=" N LEU D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 283 removed outlier: 3.653A pdb=" N MET D 283 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 328 through 344 removed outlier: 3.694A pdb=" N LEU D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N CYS D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 489 removed outlier: 4.341A pdb=" N LYS D 435 " --> pdb=" O PRO D 431 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS D 457 " --> pdb=" O SER D 453 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 removed outlier: 3.561A pdb=" N PHE D 501 " --> pdb=" O VAL D 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.871A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 248 removed outlier: 5.016A pdb=" N ILE E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 249 through 253 Processing helix chain 'E' and resid 261 through 283 removed outlier: 3.807A pdb=" N GLY E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 319 Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 337 through 344 removed outlier: 3.570A pdb=" N LEU E 343 " --> pdb=" O CYS E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 489 removed outlier: 3.677A pdb=" N LYS E 435 " --> pdb=" O PRO E 431 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 480 " --> pdb=" O SER E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.505A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.505A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLN A 79 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER A 58 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N SER A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER A 56 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N THR A 83 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 10.072A pdb=" N TYR A 54 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.525A 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: 3.735A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.943A 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: 3.735A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLU A 215 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR A 210 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 208 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.543A pdb=" N GLN B 79 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR B 83 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR B 52 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 66 removed outlier: 5.588A pdb=" N LEU B 59 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP B 77 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 61 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR B 73 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL B 65 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 71 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.785A pdb=" N GLY B 169 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.785A pdb=" N GLY B 169 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.535A pdb=" N ILE C 76 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 144 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.779A pdb=" N VAL C 71 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL C 65 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR C 73 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP C 77 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU C 59 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN C 79 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU C 57 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N SER C 81 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE C 55 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR C 83 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL C 53 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 53 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.624A pdb=" N GLY C 169 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.624A pdb=" N GLY C 169 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 208 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 102 removed outlier: 4.212A pdb=" N HIS D 137 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 79 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 66 removed outlier: 5.544A pdb=" N LEU D 59 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP D 77 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN D 61 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR D 73 " --> pdb=" O MET D 63 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL D 65 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 71 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 3.626A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 220 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 3.626A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 220 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.626A pdb=" N VAL E 100 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR E 83 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR E 52 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 59 through 66 removed outlier: 7.334A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 3.735A pdb=" N GLY E 169 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 220 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 3.735A pdb=" N GLY E 169 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 220 " --> pdb=" O PHE E 168 " (cutoff:3.500A) 895 hydrogen bonds defined for protein. 2601 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: 2.23 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2568 1.31 - 1.44: 4624 1.44 - 1.57: 9269 1.57 - 1.70: 4 1.70 - 1.83: 170 Bond restraints: 16635 Sorted by residual: bond pdb=" C6 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.37e+01 bond pdb=" C6 NCT C 601 " pdb=" N2 NCT C 601 " ideal model delta sigma weight residual 1.452 1.622 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" C6 NCT C 601 " pdb=" C7 NCT C 601 " ideal model delta sigma weight residual 1.536 1.367 0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" C6 NCT A 601 " pdb=" C7 NCT A 601 " ideal model delta sigma weight residual 1.536 1.368 0.168 2.00e-02 2.50e+03 7.04e+01 bond pdb=" C9 NCT C 601 " pdb=" N2 NCT C 601 " ideal model delta sigma weight residual 1.452 1.305 0.147 2.00e-02 2.50e+03 5.40e+01 ... (remaining 16630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 22170 1.99 - 3.98: 398 3.98 - 5.97: 105 5.97 - 7.96: 16 7.96 - 9.94: 8 Bond angle restraints: 22697 Sorted by residual: angle pdb=" CA GLU B 454 " pdb=" CB GLU B 454 " pdb=" CG GLU B 454 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" C ILE E 282 " pdb=" N MET E 283 " pdb=" CA MET E 283 " ideal model delta sigma weight residual 120.68 125.85 -5.17 1.52e+00 4.33e-01 1.16e+01 angle pdb=" N VAL E 132 " pdb=" CA VAL E 132 " pdb=" C VAL E 132 " ideal model delta sigma weight residual 108.53 113.42 -4.89 1.45e+00 4.76e-01 1.14e+01 angle pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" C5 NAG F 1 " ideal model delta sigma weight residual 109.38 119.32 -9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N MET A 283 " pdb=" CA MET A 283 " pdb=" C MET A 283 " ideal model delta sigma weight residual 109.83 114.00 -4.17 1.27e+00 6.20e-01 1.08e+01 ... (remaining 22692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8663 17.77 - 35.54: 1040 35.54 - 53.31: 277 53.31 - 71.09: 34 71.09 - 88.86: 12 Dihedral angle restraints: 10026 sinusoidal: 4131 harmonic: 5895 Sorted by residual: dihedral pdb=" CB CYS A 150 " pdb=" SG CYS A 150 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual 93.00 50.33 42.67 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CB CYS C 150 " pdb=" SG CYS C 150 " pdb=" SG CYS C 164 " pdb=" CB CYS C 164 " ideal model delta sinusoidal sigma weight residual 93.00 50.56 42.44 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CA CYS D 212 " pdb=" C CYS D 212 " pdb=" N CYS D 213 " pdb=" CA CYS D 213 " ideal model delta harmonic sigma weight residual -180.00 -155.07 -24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 10023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2302 0.066 - 0.133: 271 0.133 - 0.199: 23 0.199 - 0.265: 3 0.265 - 0.332: 3 Chirality restraints: 2602 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 133 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 2599 not shown) Planarity restraints: 2841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 176 " 0.015 2.00e-02 2.50e+03 1.27e-02 4.01e+00 pdb=" CG TRP E 176 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 176 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP E 176 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 176 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 176 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 176 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 176 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 176 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 176 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 290 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 291 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 283 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B 284 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.025 5.00e-02 4.00e+02 ... (remaining 2838 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3075 2.77 - 3.30: 14975 3.30 - 3.84: 26614 3.84 - 4.37: 29592 4.37 - 4.90: 52838 Nonbonded interactions: 127094 Sorted by model distance: nonbonded pdb=" OD1 ASN D 90 " pdb=" OG SER D 92 " model vdw 2.240 3.040 nonbonded pdb=" OG SER D 206 " pdb=" OD1 ASP D 219 " model vdw 2.261 3.040 nonbonded pdb=" OD2 ASP B 160 " pdb=" NE2 GLN B 162 " model vdw 2.261 3.120 nonbonded pdb=" N GLU B 184 " pdb=" OE1 GLU B 184 " model vdw 2.271 3.120 nonbonded pdb=" OG SER E 81 " pdb=" CE1BHIS E 137 " model vdw 2.275 3.260 ... (remaining 127089 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 346 or (resid 347 and \ (name N or name CA or name C or name O or name CB )) or resid 348 through 502)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 346 or (resid 347 and \ (name N or name CA or name C or name O or name CB )) or resid 348 through 502)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 346 or (resid 347 and \ (name N or name CA or name C or name O or name CB )) or resid 348 through 502)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 346 or (resid 347 and \ (name N or name CA or name C or name O or name CB )) or resid 348 through 502)) selection = (chain 'E' and (resid 23 through 136 or resid 138 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.960 Find NCS groups from input model: 0.600 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 0.172 16660 Z= 0.370 Angle : 0.712 10.589 22762 Z= 0.337 Chirality : 0.045 0.332 2602 Planarity : 0.004 0.047 2831 Dihedral : 16.081 88.858 6186 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.11 % Allowed : 16.84 % Favored : 83.05 % 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: 0.91 (0.19), residues: 1985 helix: 2.11 (0.18), residues: 793 sheet: 0.01 (0.25), residues: 429 loop : -0.63 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 347 TYR 0.017 0.001 TYR D 296 PHE 0.011 0.001 PHE B 462 TRP 0.034 0.001 TRP E 176 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00754 (16635) covalent geometry : angle 0.69676 (22697) SS BOND : bond 0.00689 ( 10) SS BOND : angle 1.28570 ( 20) hydrogen bonds : bond 0.13826 ( 833) hydrogen bonds : angle 5.51401 ( 2601) link_BETA1-4 : bond 0.00236 ( 5) link_BETA1-4 : angle 0.80167 ( 15) link_NAG-ASN : bond 0.00243 ( 10) link_NAG-ASN : angle 3.95373 ( 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 330 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 328 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 278 LEU cc_start: 0.8768 (tt) cc_final: 0.8495 (mp) REVERT: A 451 ASP cc_start: 0.8974 (m-30) cc_final: 0.8769 (m-30) REVERT: A 461 LYS cc_start: 0.9430 (mttt) cc_final: 0.9158 (mttm) REVERT: A 471 CYS cc_start: 0.9136 (m) cc_final: 0.8661 (t) REVERT: B 178 LEU cc_start: 0.9432 (tt) cc_final: 0.9153 (tt) REVERT: B 316 GLN cc_start: 0.8931 (pp30) cc_final: 0.8713 (tm-30) REVERT: B 438 GLU cc_start: 0.9002 (pt0) cc_final: 0.8732 (pt0) REVERT: B 441 ARG cc_start: 0.8746 (mtp180) cc_final: 0.8423 (mmm-85) REVERT: C 276 MET cc_start: 0.8556 (ttm) cc_final: 0.7560 (ppp) REVERT: C 302 ILE cc_start: 0.9305 (mm) cc_final: 0.8953 (pt) REVERT: C 439 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8649 (mm-30) REVERT: C 453 SER cc_start: 0.9237 (m) cc_final: 0.8757 (p) REVERT: D 176 TRP cc_start: 0.8595 (m100) cc_final: 0.8295 (m-90) REVERT: D 245 SER cc_start: 0.9452 (t) cc_final: 0.9190 (p) REVERT: D 262 ILE cc_start: 0.8557 (mm) cc_final: 0.8080 (mp) REVERT: D 321 ASP cc_start: 0.8492 (t70) cc_final: 0.8118 (t0) REVERT: D 432 ASP cc_start: 0.9026 (m-30) cc_final: 0.8705 (m-30) REVERT: D 435 LYS cc_start: 0.8840 (mttp) cc_final: 0.8591 (ptpt) REVERT: D 470 LEU cc_start: 0.9141 (mt) cc_final: 0.8926 (mt) REVERT: E 260 GLU cc_start: 0.8676 (pt0) cc_final: 0.8445 (pm20) REVERT: E 341 TRP cc_start: 0.6459 (t60) cc_final: 0.6249 (m-10) REVERT: E 451 ASP cc_start: 0.8564 (m-30) cc_final: 0.8253 (m-30) REVERT: E 471 CYS cc_start: 0.8873 (m) cc_final: 0.8601 (m) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.0927 time to fit residues: 47.3995 Evaluate side-chains 244 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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: 3.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN B 137 HIS A C 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.082820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.067386 restraints weight = 83482.824| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.77 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16660 Z= 0.136 Angle : 0.639 11.721 22762 Z= 0.310 Chirality : 0.045 0.544 2602 Planarity : 0.004 0.041 2831 Dihedral : 7.372 54.239 2505 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.93 % Allowed : 17.52 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1985 helix: 1.95 (0.18), residues: 827 sheet: 0.34 (0.25), residues: 439 loop : -0.61 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 347 TYR 0.011 0.001 TYR E 296 PHE 0.022 0.001 PHE C 478 TRP 0.026 0.001 TRP E 176 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00303 (16635) covalent geometry : angle 0.61346 (22697) SS BOND : bond 0.00823 ( 10) SS BOND : angle 1.74224 ( 20) hydrogen bonds : bond 0.05290 ( 833) hydrogen bonds : angle 4.49843 ( 2601) link_BETA1-4 : bond 0.00496 ( 5) link_BETA1-4 : angle 2.07359 ( 15) link_NAG-ASN : bond 0.00394 ( 10) link_NAG-ASN : angle 4.60294 ( 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 300 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8751 (tp30) cc_final: 0.8478 (tm-30) REVERT: A 327 MET cc_start: 0.8689 (ttm) cc_final: 0.7372 (ttm) REVERT: A 451 ASP cc_start: 0.8882 (m-30) cc_final: 0.8662 (m-30) REVERT: A 471 CYS cc_start: 0.8870 (m) cc_final: 0.8290 (t) REVERT: B 243 LEU cc_start: 0.9192 (mm) cc_final: 0.8695 (pp) REVERT: B 316 GLN cc_start: 0.8868 (pp30) cc_final: 0.8659 (tm-30) REVERT: B 441 ARG cc_start: 0.8712 (mtp180) cc_final: 0.8338 (mmm-85) REVERT: C 276 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7916 (ttp) REVERT: C 302 ILE cc_start: 0.9202 (mm) cc_final: 0.8759 (pt) REVERT: C 438 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: C 453 SER cc_start: 0.8863 (m) cc_final: 0.8616 (p) REVERT: D 245 SER cc_start: 0.9393 (t) cc_final: 0.9136 (p) REVERT: D 262 ILE cc_start: 0.8337 (mm) cc_final: 0.7739 (mt) REVERT: D 321 ASP cc_start: 0.8465 (t70) cc_final: 0.8046 (t0) REVERT: D 432 ASP cc_start: 0.9024 (m-30) cc_final: 0.8454 (m-30) REVERT: D 435 LYS cc_start: 0.8819 (mttp) cc_final: 0.8316 (mtmt) REVERT: D 438 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: E 341 TRP cc_start: 0.6454 (t60) cc_final: 0.6185 (m-10) REVERT: E 441 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8750 (ptp-110) REVERT: E 471 CYS cc_start: 0.8512 (m) cc_final: 0.8297 (m) outliers start: 34 outliers final: 23 residues processed: 277 average time/residue: 0.0875 time to fit residues: 38.4150 Evaluate side-chains 274 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 441 ARG Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.082444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.066664 restraints weight = 82946.092| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 4.83 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16660 Z= 0.115 Angle : 0.609 12.147 22762 Z= 0.290 Chirality : 0.044 0.512 2602 Planarity : 0.004 0.049 2831 Dihedral : 6.406 52.779 2505 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.64 % Allowed : 18.03 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 1985 helix: 2.01 (0.18), residues: 830 sheet: 0.48 (0.27), residues: 405 loop : -0.61 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 347 TYR 0.011 0.001 TYR E 296 PHE 0.017 0.001 PHE C 478 TRP 0.030 0.001 TRP E 176 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00257 (16635) covalent geometry : angle 0.58215 (22697) SS BOND : bond 0.00801 ( 10) SS BOND : angle 1.58467 ( 20) hydrogen bonds : bond 0.04766 ( 833) hydrogen bonds : angle 4.17138 ( 2601) link_BETA1-4 : bond 0.00462 ( 5) link_BETA1-4 : angle 1.99550 ( 15) link_NAG-ASN : bond 0.00334 ( 10) link_NAG-ASN : angle 4.59121 ( 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 294 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8724 (tp30) cc_final: 0.8468 (tm-30) REVERT: A 235 LEU cc_start: 0.9468 (tp) cc_final: 0.9249 (tt) REVERT: A 451 ASP cc_start: 0.8867 (m-30) cc_final: 0.8662 (m-30) REVERT: B 243 LEU cc_start: 0.9146 (mm) cc_final: 0.8681 (pp) REVERT: B 441 ARG cc_start: 0.8595 (mtp180) cc_final: 0.8226 (mmm-85) REVERT: C 276 MET cc_start: 0.8392 (ttm) cc_final: 0.7949 (ttp) REVERT: C 439 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8735 (mm-30) REVERT: C 453 SER cc_start: 0.8856 (m) cc_final: 0.8615 (p) REVERT: D 176 TRP cc_start: 0.8663 (m100) cc_final: 0.8291 (m-90) REVERT: D 245 SER cc_start: 0.9381 (t) cc_final: 0.9099 (p) REVERT: D 321 ASP cc_start: 0.8383 (t70) cc_final: 0.8020 (t0) REVERT: D 438 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: E 260 GLU cc_start: 0.8753 (pm20) cc_final: 0.7991 (pt0) REVERT: E 341 TRP cc_start: 0.6498 (t60) cc_final: 0.6228 (m-10) REVERT: E 441 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8738 (ptp-110) REVERT: E 471 CYS cc_start: 0.8534 (m) cc_final: 0.8276 (m) outliers start: 29 outliers final: 14 residues processed: 278 average time/residue: 0.0949 time to fit residues: 41.9815 Evaluate side-chains 261 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 245 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 441 ARG Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 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 316 GLN C 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.063691 restraints weight = 76147.445| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.45 r_work: 0.2672 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 16660 Z= 0.239 Angle : 0.664 12.897 22762 Z= 0.325 Chirality : 0.046 0.533 2602 Planarity : 0.004 0.037 2831 Dihedral : 6.028 58.645 2505 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.10 % Allowed : 18.42 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1985 helix: 1.92 (0.18), residues: 825 sheet: 0.41 (0.26), residues: 435 loop : -0.57 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 121 TYR 0.012 0.001 TYR E 296 PHE 0.014 0.001 PHE C 478 TRP 0.022 0.001 TRP E 176 HIS 0.009 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00552 (16635) covalent geometry : angle 0.63569 (22697) SS BOND : bond 0.00746 ( 10) SS BOND : angle 1.53108 ( 20) hydrogen bonds : bond 0.05535 ( 833) hydrogen bonds : angle 4.39089 ( 2601) link_BETA1-4 : bond 0.00353 ( 5) link_BETA1-4 : angle 1.99235 ( 15) link_NAG-ASN : bond 0.00449 ( 10) link_NAG-ASN : angle 5.00858 ( 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 269 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 437 LEU cc_start: 0.9337 (tp) cc_final: 0.9039 (tp) REVERT: A 451 ASP cc_start: 0.8905 (m-30) cc_final: 0.8627 (m-30) REVERT: A 471 CYS cc_start: 0.9068 (m) cc_final: 0.8482 (t) REVERT: B 243 LEU cc_start: 0.9146 (mm) cc_final: 0.8681 (pp) REVERT: B 441 ARG cc_start: 0.8641 (mtp180) cc_final: 0.8268 (mmm-85) REVERT: C 296 TYR cc_start: 0.8803 (t80) cc_final: 0.8170 (t80) REVERT: C 302 ILE cc_start: 0.9331 (mm) cc_final: 0.8976 (pt) REVERT: C 339 CYS cc_start: 0.9494 (m) cc_final: 0.9283 (m) REVERT: C 438 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: C 439 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8957 (mm-30) REVERT: C 453 SER cc_start: 0.9036 (m) cc_final: 0.8805 (p) REVERT: D 176 TRP cc_start: 0.8813 (m100) cc_final: 0.8232 (m-90) REVERT: D 245 SER cc_start: 0.9375 (t) cc_final: 0.9113 (p) REVERT: D 321 ASP cc_start: 0.8629 (t70) cc_final: 0.8293 (t0) REVERT: D 432 ASP cc_start: 0.8951 (m-30) cc_final: 0.8647 (m-30) REVERT: D 435 LYS cc_start: 0.8895 (mttp) cc_final: 0.8391 (mttt) REVERT: E 260 GLU cc_start: 0.9016 (pm20) cc_final: 0.8445 (pt0) REVERT: E 441 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8915 (ptp-110) outliers start: 37 outliers final: 25 residues processed: 254 average time/residue: 0.0982 time to fit residues: 40.2744 Evaluate side-chains 250 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 441 ARG Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 477 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 192 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 168 optimal weight: 0.0980 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.065432 restraints weight = 79773.046| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 4.61 r_work: 0.2702 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.003 0.037 16660 Z= 0.135 Angle : 0.607 12.336 22762 Z= 0.294 Chirality : 0.045 0.514 2602 Planarity : 0.004 0.033 2831 Dihedral : 5.765 57.379 2505 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.76 % Allowed : 18.88 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1985 helix: 2.04 (0.18), residues: 822 sheet: 0.48 (0.26), residues: 439 loop : -0.57 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.010 0.001 TYR B 317 PHE 0.011 0.001 PHE C 478 TRP 0.027 0.001 TRP E 176 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00307 (16635) covalent geometry : angle 0.57861 (22697) SS BOND : bond 0.00771 ( 10) SS BOND : angle 1.50342 ( 20) hydrogen bonds : bond 0.05057 ( 833) hydrogen bonds : angle 4.17265 ( 2601) link_BETA1-4 : bond 0.00397 ( 5) link_BETA1-4 : angle 1.83966 ( 15) link_NAG-ASN : bond 0.00207 ( 10) link_NAG-ASN : angle 4.84427 ( 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 265 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.9516 (tp) cc_final: 0.9303 (tt) REVERT: A 451 ASP cc_start: 0.8889 (m-30) cc_final: 0.8631 (m-30) REVERT: A 471 CYS cc_start: 0.9064 (m) cc_final: 0.8524 (t) REVERT: B 243 LEU cc_start: 0.9131 (mm) cc_final: 0.8667 (pp) REVERT: B 441 ARG cc_start: 0.8621 (mtp180) cc_final: 0.8257 (mmm-85) REVERT: C 302 ILE cc_start: 0.9337 (mm) cc_final: 0.8997 (pt) REVERT: C 438 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: C 439 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8924 (mm-30) REVERT: C 453 SER cc_start: 0.9014 (m) cc_final: 0.8793 (p) REVERT: D 176 TRP cc_start: 0.8789 (m100) cc_final: 0.8258 (m-90) REVERT: D 245 SER cc_start: 0.9396 (t) cc_final: 0.9123 (p) REVERT: D 321 ASP cc_start: 0.8611 (t70) cc_final: 0.8235 (t0) REVERT: D 432 ASP cc_start: 0.8933 (m-30) cc_final: 0.8468 (m-30) REVERT: D 435 LYS cc_start: 0.8959 (mttp) cc_final: 0.8723 (mtmt) REVERT: E 260 GLU cc_start: 0.9044 (pm20) cc_final: 0.8520 (pt0) REVERT: E 441 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8879 (ptp-110) outliers start: 31 outliers final: 23 residues processed: 250 average time/residue: 0.0956 time to fit residues: 38.3471 Evaluate side-chains 253 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 441 ARG Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.063178 restraints weight = 80323.635| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 4.57 r_work: 0.2650 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 16660 Z= 0.255 Angle : 0.682 12.923 22762 Z= 0.334 Chirality : 0.047 0.533 2602 Planarity : 0.004 0.034 2831 Dihedral : 5.747 43.316 2505 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.49 % Allowed : 18.99 % Favored : 78.51 % 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: 0.95 (0.19), residues: 1985 helix: 1.88 (0.18), residues: 822 sheet: 0.36 (0.26), residues: 435 loop : -0.61 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 121 TYR 0.015 0.001 TYR B 317 PHE 0.011 0.001 PHE C 478 TRP 0.024 0.001 TRP E 176 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00588 (16635) covalent geometry : angle 0.65339 (22697) SS BOND : bond 0.00736 ( 10) SS BOND : angle 1.49491 ( 20) hydrogen bonds : bond 0.05721 ( 833) hydrogen bonds : angle 4.42573 ( 2601) link_BETA1-4 : bond 0.00285 ( 5) link_BETA1-4 : angle 1.92472 ( 15) link_NAG-ASN : bond 0.00475 ( 10) link_NAG-ASN : angle 5.18051 ( 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 272 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.8841 (mt0) REVERT: A 235 LEU cc_start: 0.9506 (tp) cc_final: 0.9128 (tt) REVERT: A 451 ASP cc_start: 0.8875 (m-30) cc_final: 0.8608 (m-30) REVERT: A 471 CYS cc_start: 0.9062 (m) cc_final: 0.8477 (t) REVERT: B 441 ARG cc_start: 0.8627 (mtp180) cc_final: 0.8268 (mmm-85) REVERT: C 438 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: C 453 SER cc_start: 0.9063 (m) cc_final: 0.8839 (p) REVERT: D 195 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8417 (tm-30) REVERT: D 245 SER cc_start: 0.9398 (t) cc_final: 0.9147 (p) REVERT: D 275 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7246 (t80) REVERT: D 321 ASP cc_start: 0.8581 (t70) cc_final: 0.8248 (t0) REVERT: E 441 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8635 (ptp-110) outliers start: 44 outliers final: 33 residues processed: 252 average time/residue: 0.0953 time to fit residues: 38.2053 Evaluate side-chains 261 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 441 ARG Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 481 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 8 optimal weight: 0.0000 chunk 155 optimal weight: 7.9990 chunk 144 optimal weight: 0.5980 chunk 190 optimal weight: 0.0570 chunk 175 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 overall best weight: 1.1306 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.081745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.066105 restraints weight = 82938.334| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 4.77 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16660 Z= 0.119 Angle : 0.611 12.193 22762 Z= 0.294 Chirality : 0.044 0.495 2602 Planarity : 0.003 0.032 2831 Dihedral : 5.440 32.787 2505 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.93 % Allowed : 19.61 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 1985 helix: 2.07 (0.18), residues: 822 sheet: 0.27 (0.25), residues: 469 loop : -0.45 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 121 TYR 0.009 0.001 TYR E 296 PHE 0.009 0.001 PHE C 478 TRP 0.032 0.001 TRP E 176 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00267 (16635) covalent geometry : angle 0.58298 (22697) SS BOND : bond 0.00776 ( 10) SS BOND : angle 1.50123 ( 20) hydrogen bonds : bond 0.04882 ( 833) hydrogen bonds : angle 4.11357 ( 2601) link_BETA1-4 : bond 0.00382 ( 5) link_BETA1-4 : angle 1.74779 ( 15) link_NAG-ASN : bond 0.00331 ( 10) link_NAG-ASN : angle 4.80288 ( 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 280 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 GLN cc_start: 0.8661 (tp40) cc_final: 0.8362 (tp-100) REVERT: A 451 ASP cc_start: 0.8790 (m-30) cc_final: 0.8522 (m-30) REVERT: B 243 LEU cc_start: 0.9156 (mm) cc_final: 0.8674 (pp) REVERT: B 441 ARG cc_start: 0.8570 (mtp180) cc_final: 0.8258 (mmm-85) REVERT: C 302 ILE cc_start: 0.9231 (mm) cc_final: 0.8877 (pt) REVERT: C 453 SER cc_start: 0.8928 (m) cc_final: 0.8694 (p) REVERT: D 176 TRP cc_start: 0.8652 (m100) cc_final: 0.8235 (m-90) REVERT: D 245 SER cc_start: 0.9387 (t) cc_final: 0.9130 (p) REVERT: D 275 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7274 (t80) REVERT: D 321 ASP cc_start: 0.8372 (t70) cc_final: 0.7985 (t0) REVERT: E 217 TYR cc_start: 0.7589 (m-10) cc_final: 0.7161 (m-10) outliers start: 34 outliers final: 24 residues processed: 260 average time/residue: 0.0997 time to fit residues: 41.4153 Evaluate side-chains 260 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 146 optimal weight: 0.0030 chunk 190 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.081605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.066343 restraints weight = 81678.812| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 4.66 r_work: 0.2715 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16660 Z= 0.124 Angle : 0.619 11.940 22762 Z= 0.295 Chirality : 0.044 0.500 2602 Planarity : 0.003 0.035 2831 Dihedral : 5.234 32.342 2505 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.59 % Allowed : 20.29 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1985 helix: 2.05 (0.18), residues: 825 sheet: 0.32 (0.25), residues: 469 loop : -0.39 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 121 TYR 0.008 0.001 TYR E 296 PHE 0.009 0.001 PHE C 478 TRP 0.030 0.001 TRP E 176 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00282 (16635) covalent geometry : angle 0.59287 (22697) SS BOND : bond 0.00785 ( 10) SS BOND : angle 1.48706 ( 20) hydrogen bonds : bond 0.04710 ( 833) hydrogen bonds : angle 4.06287 ( 2601) link_BETA1-4 : bond 0.00410 ( 5) link_BETA1-4 : angle 1.82107 ( 15) link_NAG-ASN : bond 0.00190 ( 10) link_NAG-ASN : angle 4.67489 ( 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 268 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.9149 (tp30) cc_final: 0.8659 (tm-30) REVERT: A 64 ASP cc_start: 0.8369 (t0) cc_final: 0.8070 (t0) REVERT: A 235 LEU cc_start: 0.9501 (tp) cc_final: 0.9288 (tt) REVERT: A 316 GLN cc_start: 0.8959 (tp40) cc_final: 0.8726 (tp-100) REVERT: A 451 ASP cc_start: 0.8842 (m-30) cc_final: 0.8580 (m-30) REVERT: B 441 ARG cc_start: 0.8592 (mtp180) cc_final: 0.8250 (mmm-85) REVERT: C 302 ILE cc_start: 0.9342 (mm) cc_final: 0.9012 (pt) REVERT: C 453 SER cc_start: 0.9024 (m) cc_final: 0.8776 (p) REVERT: D 176 TRP cc_start: 0.8786 (m100) cc_final: 0.8241 (m-90) REVERT: D 245 SER cc_start: 0.9381 (t) cc_final: 0.9100 (p) REVERT: D 275 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7278 (t80) REVERT: D 321 ASP cc_start: 0.8532 (t70) cc_final: 0.8162 (t0) REVERT: D 342 PHE cc_start: 0.4260 (m-80) cc_final: 0.3841 (m-80) REVERT: E 217 TYR cc_start: 0.7876 (m-10) cc_final: 0.7416 (m-10) REVERT: E 441 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8805 (ptp-110) outliers start: 28 outliers final: 22 residues processed: 253 average time/residue: 0.1046 time to fit residues: 42.5127 Evaluate side-chains 263 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 441 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9442 > 50: distance: 43 - 59: 18.218 distance: 50 - 70: 35.888 distance: 54 - 59: 15.387 distance: 59 - 60: 22.537 distance: 60 - 61: 31.328 distance: 60 - 63: 20.044 distance: 61 - 62: 5.220 distance: 61 - 70: 52.634 distance: 63 - 64: 11.919 distance: 64 - 65: 22.127 distance: 64 - 66: 17.895 distance: 65 - 67: 4.582 distance: 66 - 68: 22.230 distance: 67 - 69: 23.503 distance: 68 - 69: 17.484 distance: 71 - 72: 41.599 distance: 71 - 74: 16.373 distance: 72 - 73: 31.427 distance: 72 - 78: 8.006 distance: 74 - 75: 25.598 distance: 75 - 76: 38.603 distance: 75 - 77: 40.574 distance: 78 - 79: 11.271 distance: 79 - 80: 44.869 distance: 79 - 82: 50.036 distance: 80 - 81: 15.407 distance: 80 - 86: 38.537 distance: 82 - 83: 52.073 distance: 83 - 84: 44.842 distance: 83 - 85: 42.008 distance: 86 - 87: 34.674 distance: 86 - 92: 4.917 distance: 87 - 90: 37.883 distance: 88 - 93: 42.208 distance: 90 - 91: 3.324 distance: 93 - 94: 33.081 distance: 94 - 97: 39.388 distance: 95 - 96: 40.869 distance: 95 - 98: 40.431 distance: 98 - 99: 30.219 distance: 99 - 100: 22.714 distance: 99 - 102: 16.857 distance: 100 - 101: 23.378 distance: 100 - 106: 9.621 distance: 102 - 103: 10.111 distance: 103 - 104: 5.877 distance: 103 - 105: 12.035 distance: 106 - 107: 9.516 distance: 107 - 108: 4.232 distance: 107 - 110: 15.401 distance: 108 - 109: 46.443 distance: 108 - 112: 29.887 distance: 110 - 111: 37.321 distance: 112 - 113: 20.385 distance: 113 - 114: 13.249 distance: 114 - 115: 33.417 distance: 114 - 116: 24.673 distance: 116 - 117: 40.418 distance: 117 - 118: 17.428 distance: 117 - 120: 37.280 distance: 118 - 125: 8.830 distance: 120 - 121: 32.109 distance: 121 - 122: 12.833 distance: 122 - 123: 9.901 distance: 122 - 124: 14.435 distance: 125 - 126: 33.942 distance: 126 - 127: 9.207 distance: 126 - 129: 10.105 distance: 127 - 128: 6.539 distance: 127 - 134: 29.174 distance: 129 - 130: 7.154 distance: 130 - 131: 16.026 distance: 131 - 132: 10.283 distance: 132 - 133: 24.518