Starting phenix.real_space_refine on Tue Aug 26 22:19:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cwy_27031/08_2025/8cwy_27031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cwy_27031/08_2025/8cwy_27031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cwy_27031/08_2025/8cwy_27031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cwy_27031/08_2025/8cwy_27031.map" model { file = "/net/cci-nas-00/data/ceres_data/8cwy_27031/08_2025/8cwy_27031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cwy_27031/08_2025/8cwy_27031.cif" } resolution = 3.34 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= -0.002 sd= 0.045 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 84 5.16 5 C 28056 2.51 5 N 8124 2.21 5 O 7356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43620 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "C" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "D" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "E" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "G" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "H" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "I" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "J" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "K" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "L" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "M" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "N" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "O" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "P" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "Q" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "R" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "S" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "T" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "U" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "V" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "W" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3003 Classifications: {'peptide': 451} Incomplete info: {'n_c_alpha_c_only': 5} Link IDs: {'PTRANS': 1, 'TRANS': 449} Unresolved chain link angles: 124 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "X" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 632 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Time building chain proxies: 10.34, per 1000 atoms: 0.24 Number of scatterers: 43620 At special positions: 0 Unit cell: (192.386, 190.328, 182.098, 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 84 16.00 O 7356 8.00 N 8124 7.00 C 28056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12192 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 148 through 171 Processing helix chain 'A' and resid 173 through 196 Processing helix chain 'A' and resid 198 through 220 Processing helix chain 'A' and resid 222 through 246 removed outlier: 4.061A pdb=" N GLU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 273 through 296 Processing helix chain 'A' and resid 298 through 321 Processing helix chain 'A' and resid 323 through 345 Processing helix chain 'A' and resid 348 through 370 removed outlier: 3.528A pdb=" N ILE A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 413 Processing helix chain 'A' and resid 415 through 450 Processing helix chain 'B' and resid 453 through 488 removed outlier: 3.828A pdb=" N ILE B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 525 removed outlier: 3.657A pdb=" N GLU B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 148 through 171 Processing helix chain 'C' and resid 173 through 196 Processing helix chain 'C' and resid 198 through 221 Processing helix chain 'C' and resid 222 through 246 removed outlier: 4.055A pdb=" N GLU C 226 " --> pdb=" O THR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 273 through 296 Processing helix chain 'C' and resid 298 through 321 Processing helix chain 'C' and resid 323 through 345 Processing helix chain 'C' and resid 348 through 371 removed outlier: 3.686A pdb=" N ILE C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 413 Processing helix chain 'C' and resid 415 through 450 Processing helix chain 'D' and resid 453 through 488 removed outlier: 3.838A pdb=" N ILE D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 525 removed outlier: 3.702A pdb=" N GLU D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 148 through 171 Processing helix chain 'E' and resid 173 through 196 Processing helix chain 'E' and resid 198 through 220 Processing helix chain 'E' and resid 222 through 246 removed outlier: 4.082A pdb=" N GLU E 226 " --> pdb=" O THR E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 273 through 296 Processing helix chain 'E' and resid 298 through 321 Processing helix chain 'E' and resid 323 through 345 Processing helix chain 'E' and resid 348 through 371 removed outlier: 3.648A pdb=" N ILE E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 413 Processing helix chain 'E' and resid 415 through 450 Processing helix chain 'F' and resid 453 through 488 removed outlier: 3.808A pdb=" N ILE F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 525 removed outlier: 3.618A pdb=" N GLU F 503 " --> pdb=" O LEU F 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 146 Processing helix chain 'G' and resid 148 through 171 Processing helix chain 'G' and resid 173 through 196 Processing helix chain 'G' and resid 198 through 221 Processing helix chain 'G' and resid 222 through 246 removed outlier: 4.056A pdb=" N GLU G 226 " --> pdb=" O THR G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 271 Processing helix chain 'G' and resid 273 through 296 Processing helix chain 'G' and resid 298 through 321 Processing helix chain 'G' and resid 323 through 345 Processing helix chain 'G' and resid 348 through 371 removed outlier: 3.606A pdb=" N ILE G 352 " --> pdb=" O ASP G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 413 Processing helix chain 'G' and resid 415 through 450 Processing helix chain 'H' and resid 453 through 488 removed outlier: 3.817A pdb=" N ILE H 457 " --> pdb=" O ARG H 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 525 removed outlier: 3.687A pdb=" N GLU H 503 " --> pdb=" O LEU H 499 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 146 Processing helix chain 'I' and resid 148 through 171 Processing helix chain 'I' and resid 173 through 196 Processing helix chain 'I' and resid 198 through 220 Processing helix chain 'I' and resid 222 through 246 removed outlier: 4.056A pdb=" N GLU I 226 " --> pdb=" O THR I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 271 Processing helix chain 'I' and resid 273 through 296 Processing helix chain 'I' and resid 298 through 321 Processing helix chain 'I' and resid 323 through 345 Processing helix chain 'I' and resid 348 through 371 removed outlier: 3.638A pdb=" N ILE I 352 " --> pdb=" O ASP I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 413 Processing helix chain 'I' and resid 415 through 450 Processing helix chain 'J' and resid 453 through 488 removed outlier: 3.845A pdb=" N ILE J 457 " --> pdb=" O ARG J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 490 through 525 removed outlier: 3.711A pdb=" N GLU J 503 " --> pdb=" O LEU J 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 146 Processing helix chain 'K' and resid 148 through 171 Processing helix chain 'K' and resid 173 through 196 Processing helix chain 'K' and resid 198 through 220 Processing helix chain 'K' and resid 222 through 246 removed outlier: 4.071A pdb=" N GLU K 226 " --> pdb=" O THR K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 271 Processing helix chain 'K' and resid 273 through 296 Processing helix chain 'K' and resid 298 through 321 Processing helix chain 'K' and resid 323 through 345 Processing helix chain 'K' and resid 348 through 370 removed outlier: 3.572A pdb=" N ILE K 352 " --> pdb=" O ASP K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 373 through 413 Processing helix chain 'K' and resid 415 through 450 Processing helix chain 'L' and resid 453 through 488 removed outlier: 3.838A pdb=" N ILE L 457 " --> pdb=" O ARG L 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 490 through 525 removed outlier: 3.654A pdb=" N GLU L 503 " --> pdb=" O LEU L 499 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 146 Processing helix chain 'M' and resid 148 through 171 Processing helix chain 'M' and resid 173 through 196 Processing helix chain 'M' and resid 198 through 221 Processing helix chain 'M' and resid 222 through 246 removed outlier: 4.057A pdb=" N GLU M 226 " --> pdb=" O THR M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 271 Processing helix chain 'M' and resid 273 through 296 Processing helix chain 'M' and resid 298 through 321 Processing helix chain 'M' and resid 323 through 345 Processing helix chain 'M' and resid 348 through 371 removed outlier: 3.592A pdb=" N ILE M 352 " --> pdb=" O ASP M 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 413 Processing helix chain 'M' and resid 415 through 450 Processing helix chain 'N' and resid 453 through 488 removed outlier: 3.862A pdb=" N ILE N 457 " --> pdb=" O ARG N 453 " (cutoff:3.500A) Processing helix chain 'N' and resid 490 through 525 removed outlier: 3.699A pdb=" N GLU N 503 " --> pdb=" O LEU N 499 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 146 Processing helix chain 'O' and resid 148 through 171 Processing helix chain 'O' and resid 173 through 196 Processing helix chain 'O' and resid 198 through 220 Processing helix chain 'O' and resid 222 through 246 removed outlier: 4.064A pdb=" N GLU O 226 " --> pdb=" O THR O 222 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 271 Processing helix chain 'O' and resid 273 through 296 Processing helix chain 'O' and resid 298 through 321 Processing helix chain 'O' and resid 323 through 345 Processing helix chain 'O' and resid 348 through 371 removed outlier: 3.605A pdb=" N ILE O 352 " --> pdb=" O ASP O 348 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 413 Processing helix chain 'O' and resid 415 through 450 Processing helix chain 'P' and resid 453 through 488 removed outlier: 3.869A pdb=" N ILE P 457 " --> pdb=" O ARG P 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 490 through 525 removed outlier: 3.653A pdb=" N GLU P 503 " --> pdb=" O LEU P 499 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 146 Processing helix chain 'Q' and resid 148 through 171 Processing helix chain 'Q' and resid 173 through 196 Processing helix chain 'Q' and resid 198 through 221 Processing helix chain 'Q' and resid 222 through 246 removed outlier: 4.065A pdb=" N GLU Q 226 " --> pdb=" O THR Q 222 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 271 Processing helix chain 'Q' and resid 273 through 296 Processing helix chain 'Q' and resid 298 through 321 Processing helix chain 'Q' and resid 323 through 345 Processing helix chain 'Q' and resid 348 through 371 removed outlier: 3.542A pdb=" N ILE Q 352 " --> pdb=" O ASP Q 348 " (cutoff:3.500A) Processing helix chain 'Q' and resid 373 through 413 Processing helix chain 'Q' and resid 415 through 450 Processing helix chain 'R' and resid 453 through 488 removed outlier: 3.809A pdb=" N ILE R 457 " --> pdb=" O ARG R 453 " (cutoff:3.500A) Processing helix chain 'R' and resid 490 through 525 removed outlier: 3.732A pdb=" N GLU R 503 " --> pdb=" O LEU R 499 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 146 Processing helix chain 'S' and resid 148 through 171 Processing helix chain 'S' and resid 173 through 196 Processing helix chain 'S' and resid 198 through 221 Processing helix chain 'S' and resid 222 through 246 removed outlier: 4.068A pdb=" N GLU S 226 " --> pdb=" O THR S 222 " (cutoff:3.500A) Processing helix chain 'S' and resid 248 through 271 Processing helix chain 'S' and resid 273 through 296 Processing helix chain 'S' and resid 298 through 321 Processing helix chain 'S' and resid 323 through 345 Processing helix chain 'S' and resid 348 through 371 removed outlier: 3.576A pdb=" N ILE S 352 " --> pdb=" O ASP S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 373 through 413 Processing helix chain 'S' and resid 415 through 450 Processing helix chain 'T' and resid 453 through 488 removed outlier: 3.838A pdb=" N ILE T 457 " --> pdb=" O ARG T 453 " (cutoff:3.500A) Processing helix chain 'T' and resid 490 through 525 removed outlier: 3.684A pdb=" N GLU T 503 " --> pdb=" O LEU T 499 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 146 Processing helix chain 'U' and resid 148 through 171 Processing helix chain 'U' and resid 173 through 196 Processing helix chain 'U' and resid 198 through 221 Processing helix chain 'U' and resid 222 through 246 removed outlier: 4.044A pdb=" N GLU U 226 " --> pdb=" O THR U 222 " (cutoff:3.500A) Processing helix chain 'U' and resid 248 through 271 Processing helix chain 'U' and resid 273 through 296 Processing helix chain 'U' and resid 298 through 321 Processing helix chain 'U' and resid 323 through 345 Processing helix chain 'U' and resid 348 through 371 removed outlier: 3.563A pdb=" N ILE U 352 " --> pdb=" O ASP U 348 " (cutoff:3.500A) Processing helix chain 'U' and resid 373 through 413 Processing helix chain 'U' and resid 415 through 450 Processing helix chain 'V' and resid 453 through 488 removed outlier: 3.809A pdb=" N ILE V 457 " --> pdb=" O ARG V 453 " (cutoff:3.500A) Processing helix chain 'V' and resid 490 through 525 removed outlier: 3.672A pdb=" N GLU V 503 " --> pdb=" O LEU V 499 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 146 Processing helix chain 'W' and resid 148 through 171 Processing helix chain 'W' and resid 173 through 196 Processing helix chain 'W' and resid 198 through 221 Processing helix chain 'W' and resid 222 through 246 removed outlier: 4.038A pdb=" N GLU W 226 " --> pdb=" O THR W 222 " (cutoff:3.500A) Processing helix chain 'W' and resid 248 through 271 Processing helix chain 'W' and resid 273 through 296 Processing helix chain 'W' and resid 298 through 321 Processing helix chain 'W' and resid 323 through 345 Processing helix chain 'W' and resid 348 through 371 removed outlier: 3.666A pdb=" N ILE W 352 " --> pdb=" O ASP W 348 " (cutoff:3.500A) Processing helix chain 'W' and resid 373 through 413 Processing helix chain 'W' and resid 415 through 450 Processing helix chain 'X' and resid 453 through 488 removed outlier: 3.866A pdb=" N ILE X 457 " --> pdb=" O ARG X 453 " (cutoff:3.500A) Processing helix chain 'X' and resid 490 through 525 removed outlier: 3.633A pdb=" N GLU X 503 " --> pdb=" O LEU X 499 " (cutoff:3.500A) 3917 hydrogen bonds defined for protein. 11751 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: 8.40 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14628 1.34 - 1.46: 1868 1.46 - 1.57: 27028 1.57 - 1.69: 0 1.69 - 1.80: 168 Bond restraints: 43692 Sorted by residual: bond pdb=" CG LEU F 482 " pdb=" CD1 LEU F 482 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.46e-01 bond pdb=" CG LEU V 482 " pdb=" CD1 LEU V 482 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.34e-01 bond pdb=" CG LEU D 482 " pdb=" CD1 LEU D 482 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.20e-01 bond pdb=" CG LEU R 482 " pdb=" CD1 LEU R 482 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.09e-01 bond pdb=" CG LEU T 482 " pdb=" CD1 LEU T 482 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.00e-01 ... (remaining 43687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.58: 54170 0.58 - 1.16: 3465 1.16 - 1.75: 427 1.75 - 2.33: 87 2.33 - 2.91: 27 Bond angle restraints: 58176 Sorted by residual: angle pdb=" N MET H 498 " pdb=" CA MET H 498 " pdb=" C MET H 498 " ideal model delta sigma weight residual 112.54 110.94 1.60 1.22e+00 6.72e-01 1.72e+00 angle pdb=" N MET R 498 " pdb=" CA MET R 498 " pdb=" C MET R 498 " ideal model delta sigma weight residual 112.54 110.94 1.60 1.22e+00 6.72e-01 1.72e+00 angle pdb=" N MET P 498 " pdb=" CA MET P 498 " pdb=" C MET P 498 " ideal model delta sigma weight residual 112.38 110.84 1.54 1.22e+00 6.72e-01 1.60e+00 angle pdb=" N MET D 498 " pdb=" CA MET D 498 " pdb=" C MET D 498 " ideal model delta sigma weight residual 112.38 110.84 1.54 1.22e+00 6.72e-01 1.60e+00 angle pdb=" N MET N 498 " pdb=" CA MET N 498 " pdb=" C MET N 498 " ideal model delta sigma weight residual 112.38 110.84 1.54 1.22e+00 6.72e-01 1.59e+00 ... (remaining 58171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.64: 26589 11.64 - 23.28: 1646 23.28 - 34.92: 276 34.92 - 46.55: 78 46.55 - 58.19: 7 Dihedral angle restraints: 28596 sinusoidal: 10092 harmonic: 18504 Sorted by residual: dihedral pdb=" CB MET S 378 " pdb=" CG MET S 378 " pdb=" SD MET S 378 " pdb=" CE MET S 378 " ideal model delta sinusoidal sigma weight residual -60.00 -118.19 58.19 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET U 378 " pdb=" CG MET U 378 " pdb=" SD MET U 378 " pdb=" CE MET U 378 " ideal model delta sinusoidal sigma weight residual -60.00 -114.70 54.70 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CB MET G 378 " pdb=" CG MET G 378 " pdb=" SD MET G 378 " pdb=" CE MET G 378 " ideal model delta sinusoidal sigma weight residual -60.00 -114.67 54.67 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 28593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 5278 0.022 - 0.043: 1159 0.043 - 0.065: 804 0.065 - 0.086: 692 0.086 - 0.108: 47 Chirality restraints: 7980 Sorted by residual: chirality pdb=" CA VAL I 372 " pdb=" N VAL I 372 " pdb=" C VAL I 372 " pdb=" CB VAL I 372 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.90e-01 chirality pdb=" CA VAL M 372 " pdb=" N VAL M 372 " pdb=" C VAL M 372 " pdb=" CB VAL M 372 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.76e-01 chirality pdb=" CA VAL A 372 " pdb=" N VAL A 372 " pdb=" C VAL A 372 " pdb=" CB VAL A 372 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.68e-01 ... (remaining 7977 not shown) Planarity restraints: 6396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU K 389 " 0.003 2.00e-02 2.50e+03 5.84e-03 3.41e-01 pdb=" C LEU K 389 " -0.010 2.00e-02 2.50e+03 pdb=" O LEU K 389 " 0.004 2.00e-02 2.50e+03 pdb=" N ARG K 390 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 389 " 0.003 2.00e-02 2.50e+03 5.79e-03 3.35e-01 pdb=" C LEU C 389 " -0.010 2.00e-02 2.50e+03 pdb=" O LEU C 389 " 0.004 2.00e-02 2.50e+03 pdb=" N ARG C 390 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU O 389 " -0.003 2.00e-02 2.50e+03 5.76e-03 3.32e-01 pdb=" C LEU O 389 " 0.010 2.00e-02 2.50e+03 pdb=" O LEU O 389 " -0.004 2.00e-02 2.50e+03 pdb=" N ARG O 390 " -0.003 2.00e-02 2.50e+03 ... (remaining 6393 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 300 2.60 - 3.18: 39183 3.18 - 3.75: 63486 3.75 - 4.33: 84149 4.33 - 4.90: 155554 Nonbonded interactions: 342672 Sorted by model distance: nonbonded pdb=" OG SER S 248 " pdb=" OE2 GLU T 506 " model vdw 2.026 3.040 nonbonded pdb=" OG SER Q 248 " pdb=" OE2 GLU R 506 " model vdw 2.028 3.040 nonbonded pdb=" OG SER W 186 " pdb=" NH1 ARG W 190 " model vdw 2.185 3.120 nonbonded pdb=" OG SER U 186 " pdb=" NH1 ARG U 190 " model vdw 2.187 3.120 nonbonded pdb=" OG SER K 186 " pdb=" NH1 ARG K 190 " model vdw 2.192 3.120 ... (remaining 342667 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 39.680 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 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 : 0.002 0.022 43692 Z= 0.112 Angle : 0.319 2.909 58176 Z= 0.196 Chirality : 0.032 0.108 7980 Planarity : 0.002 0.019 6396 Dihedral : 8.096 58.192 16404 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.02 % Allowed : 0.84 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.71 (0.09), residues: 6252 helix: 3.82 (0.06), residues: 5916 sheet: None (None), residues: 0 loop : 1.18 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.003 0.001 TYR D 517 PHE 0.009 0.001 PHE O 435 HIS 0.001 0.000 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00243 (43692) covalent geometry : angle 0.31944 (58176) hydrogen bonds : bond 0.13262 ( 3917) hydrogen bonds : angle 4.14830 (11751) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 503 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7375 (tpt90) cc_final: 0.7053 (tpt170) REVERT: C 283 ARG cc_start: 0.7458 (tpt90) cc_final: 0.7159 (tpt170) REVERT: D 475 MET cc_start: 0.8018 (tpp) cc_final: 0.7205 (tpt) REVERT: E 449 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7706 (mtm-85) REVERT: G 449 ARG cc_start: 0.8028 (mtm110) cc_final: 0.7778 (mtm110) REVERT: H 498 MET cc_start: 0.8011 (mmm) cc_final: 0.7560 (tpt) REVERT: I 283 ARG cc_start: 0.7263 (tpt90) cc_final: 0.6503 (tpt170) REVERT: I 378 MET cc_start: 0.6544 (tpt) cc_final: 0.6012 (tpt) REVERT: K 233 ARG cc_start: 0.7253 (tpt170) cc_final: 0.6482 (tpt170) REVERT: K 283 ARG cc_start: 0.7426 (tpt90) cc_final: 0.6990 (tpt170) REVERT: M 283 ARG cc_start: 0.7367 (tpt90) cc_final: 0.7022 (tpt170) REVERT: M 378 MET cc_start: 0.6500 (tpt) cc_final: 0.6126 (tpt) REVERT: O 283 ARG cc_start: 0.7410 (tpt90) cc_final: 0.7057 (tpt170) REVERT: O 378 MET cc_start: 0.6389 (tpt) cc_final: 0.6021 (tpt) REVERT: Q 283 ARG cc_start: 0.7462 (tpt90) cc_final: 0.6982 (tpt170) REVERT: Q 378 MET cc_start: 0.6724 (tpt) cc_final: 0.6003 (tpt) REVERT: S 283 ARG cc_start: 0.7366 (tpt90) cc_final: 0.6967 (tpt170) REVERT: T 500 ARG cc_start: 0.8427 (mtp180) cc_final: 0.8203 (mtp180) REVERT: V 500 ARG cc_start: 0.8386 (mtp180) cc_final: 0.8054 (mtp180) outliers start: 1 outliers final: 1 residues processed: 504 average time/residue: 0.4330 time to fit residues: 310.8552 Evaluate side-chains 378 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 451 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 50.0000 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 0.5980 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 30.0000 chunk 597 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.246036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.194080 restraints weight = 44270.670| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.35 r_work: 0.3580 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 43692 Z= 0.172 Angle : 0.458 5.821 58176 Z= 0.237 Chirality : 0.034 0.124 7980 Planarity : 0.003 0.053 6396 Dihedral : 2.605 34.276 6806 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.38 % Allowed : 3.33 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.14 (0.09), residues: 6252 helix: 4.11 (0.06), residues: 5892 sheet: None (None), residues: 0 loop : 1.15 (0.23), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 190 TYR 0.022 0.002 TYR P 517 PHE 0.007 0.002 PHE Q 435 HIS 0.004 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00440 (43692) covalent geometry : angle 0.45783 (58176) hydrogen bonds : bond 0.05178 ( 3917) hydrogen bonds : angle 3.16676 (11751) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 404 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.7934 (tpt170) cc_final: 0.7665 (tpt170) REVERT: A 283 ARG cc_start: 0.7731 (tpt90) cc_final: 0.7220 (tpp80) REVERT: A 442 LEU cc_start: 0.8688 (mt) cc_final: 0.8424 (mp) REVERT: B 523 LYS cc_start: 0.6162 (ptpt) cc_final: 0.5231 (ptpp) REVERT: C 183 ARG cc_start: 0.7092 (tpt90) cc_final: 0.6891 (mmm-85) REVERT: C 190 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6943 (mtm110) REVERT: C 243 LYS cc_start: 0.8276 (tppp) cc_final: 0.7567 (mmtt) REVERT: C 283 ARG cc_start: 0.7907 (tpt90) cc_final: 0.7142 (tpt170) REVERT: C 287 GLU cc_start: 0.8197 (tp30) cc_final: 0.7718 (tp30) REVERT: E 340 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7812 (mtm110) REVERT: F 485 GLN cc_start: 0.8904 (mt0) cc_final: 0.8646 (mt0) REVERT: G 233 ARG cc_start: 0.7893 (tpt170) cc_final: 0.7587 (tpt170) REVERT: H 517 TYR cc_start: 0.7869 (t80) cc_final: 0.7574 (t80) REVERT: I 243 LYS cc_start: 0.8357 (tppt) cc_final: 0.7788 (mmtt) REVERT: I 283 ARG cc_start: 0.7834 (tpt90) cc_final: 0.7471 (tpt170) REVERT: I 378 MET cc_start: 0.7895 (tpt) cc_final: 0.6984 (tpt) REVERT: K 233 ARG cc_start: 0.7954 (tpt170) cc_final: 0.7731 (tpt170) REVERT: K 283 ARG cc_start: 0.7858 (tpt90) cc_final: 0.7269 (tpp80) REVERT: M 283 ARG cc_start: 0.7674 (tpt90) cc_final: 0.7122 (tpp80) REVERT: O 283 ARG cc_start: 0.7851 (tpt90) cc_final: 0.7313 (tpt170) REVERT: O 340 ARG cc_start: 0.8267 (mtm110) cc_final: 0.8030 (mtm110) REVERT: R 485 GLN cc_start: 0.8810 (mt0) cc_final: 0.8532 (mt0) REVERT: S 283 ARG cc_start: 0.7843 (tpt90) cc_final: 0.7326 (tpt170) REVERT: S 449 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8122 (ttm170) REVERT: W 378 MET cc_start: 0.7659 (tpt) cc_final: 0.6762 (mtt) outliers start: 16 outliers final: 8 residues processed: 411 average time/residue: 0.4073 time to fit residues: 244.2334 Evaluate side-chains 370 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 362 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain X residue 486 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 345 optimal weight: 0.7980 chunk 622 optimal weight: 4.9990 chunk 262 optimal weight: 50.0000 chunk 96 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 405 optimal weight: 7.9990 chunk 427 optimal weight: 50.0000 chunk 237 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.246742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.194596 restraints weight = 44152.728| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.32 r_work: 0.3579 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 43692 Z= 0.150 Angle : 0.416 9.626 58176 Z= 0.217 Chirality : 0.033 0.122 7980 Planarity : 0.002 0.039 6396 Dihedral : 2.551 31.921 6806 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.84 % Allowed : 3.74 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.23 (0.09), residues: 6252 helix: 4.18 (0.06), residues: 5916 sheet: None (None), residues: 0 loop : 0.68 (0.20), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 190 TYR 0.021 0.002 TYR P 517 PHE 0.008 0.001 PHE Q 435 HIS 0.004 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00380 (43692) covalent geometry : angle 0.41620 (58176) hydrogen bonds : bond 0.04766 ( 3917) hydrogen bonds : angle 3.01809 (11751) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 396 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7745 (tpt170) REVERT: A 283 ARG cc_start: 0.7824 (tpt90) cc_final: 0.7326 (tpp80) REVERT: A 378 MET cc_start: 0.7699 (tpt) cc_final: 0.7004 (mtt) REVERT: A 442 LEU cc_start: 0.8702 (mt) cc_final: 0.8452 (mp) REVERT: C 183 ARG cc_start: 0.7085 (tpt90) cc_final: 0.6872 (mmm-85) REVERT: C 243 LYS cc_start: 0.8340 (tppp) cc_final: 0.7621 (mmtt) REVERT: C 283 ARG cc_start: 0.8006 (tpt90) cc_final: 0.7637 (tpt170) REVERT: F 485 GLN cc_start: 0.8881 (mt0) cc_final: 0.8635 (mt0) REVERT: G 233 ARG cc_start: 0.8054 (tpt170) cc_final: 0.7832 (tpt170) REVERT: G 240 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7426 (ttp-110) REVERT: I 183 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.6999 (tpp80) REVERT: I 243 LYS cc_start: 0.8361 (tppt) cc_final: 0.7810 (mmtt) REVERT: I 283 ARG cc_start: 0.7891 (tpt90) cc_final: 0.7360 (tpp80) REVERT: I 335 MET cc_start: 0.8338 (mtp) cc_final: 0.8124 (mtm) REVERT: I 378 MET cc_start: 0.7762 (tpt) cc_final: 0.6844 (tpt) REVERT: K 233 ARG cc_start: 0.8063 (tpt170) cc_final: 0.7814 (tpt170) REVERT: K 283 ARG cc_start: 0.7841 (tpt90) cc_final: 0.7287 (tpp80) REVERT: K 287 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7905 (mm-30) REVERT: M 190 ARG cc_start: 0.7397 (mtm110) cc_final: 0.7189 (mtm110) REVERT: M 283 ARG cc_start: 0.7705 (tpt90) cc_final: 0.7201 (tpp80) REVERT: O 283 ARG cc_start: 0.7959 (tpt90) cc_final: 0.7428 (tpt170) REVERT: O 340 ARG cc_start: 0.8296 (mtm110) cc_final: 0.8071 (mtm110) REVERT: O 378 MET cc_start: 0.7649 (tpt) cc_final: 0.7028 (mtt) REVERT: Q 183 ARG cc_start: 0.7393 (tpp80) cc_final: 0.6845 (tpt90) REVERT: Q 240 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7669 (ttp80) REVERT: R 485 GLN cc_start: 0.8800 (mt0) cc_final: 0.8413 (mt0) REVERT: S 283 ARG cc_start: 0.7938 (tpt90) cc_final: 0.7453 (tpt170) REVERT: S 449 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.8044 (ttm170) REVERT: U 340 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7807 (mtm110) REVERT: W 183 ARG cc_start: 0.7283 (tpp80) cc_final: 0.6677 (tpt-90) REVERT: W 378 MET cc_start: 0.7559 (tpt) cc_final: 0.6741 (mtt) outliers start: 35 outliers final: 18 residues processed: 419 average time/residue: 0.3907 time to fit residues: 240.4295 Evaluate side-chains 378 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 360 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain U residue 345 SER Chi-restraints excluded: chain V residue 486 MET Chi-restraints excluded: chain X residue 486 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 113 optimal weight: 50.0000 chunk 477 optimal weight: 50.0000 chunk 132 optimal weight: 0.5980 chunk 277 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 270 optimal weight: 80.0000 chunk 606 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 577 optimal weight: 50.0000 chunk 426 optimal weight: 80.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.244354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.193568 restraints weight = 44213.023| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.21 r_work: 0.3582 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 43692 Z= 0.196 Angle : 0.469 8.079 58176 Z= 0.242 Chirality : 0.034 0.143 7980 Planarity : 0.002 0.034 6396 Dihedral : 2.684 38.477 6806 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.53 % Allowed : 4.89 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.97 (0.09), residues: 6252 helix: 4.02 (0.06), residues: 5892 sheet: None (None), residues: 0 loop : 0.79 (0.23), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 340 TYR 0.022 0.002 TYR T 517 PHE 0.012 0.002 PHE U 435 HIS 0.004 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00515 (43692) covalent geometry : angle 0.46932 (58176) hydrogen bonds : bond 0.05280 ( 3917) hydrogen bonds : angle 3.11272 (11751) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 381 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7195 (tpp80) cc_final: 0.6703 (tpt90) REVERT: A 233 ARG cc_start: 0.8059 (tpt170) cc_final: 0.7757 (tpt170) REVERT: A 283 ARG cc_start: 0.7814 (tpt90) cc_final: 0.7272 (tpp80) REVERT: A 442 LEU cc_start: 0.8709 (mt) cc_final: 0.8489 (mp) REVERT: C 183 ARG cc_start: 0.7278 (tpt90) cc_final: 0.7049 (mmm-85) REVERT: C 243 LYS cc_start: 0.8438 (tppp) cc_final: 0.7770 (mmtt) REVERT: C 283 ARG cc_start: 0.8055 (tpt90) cc_final: 0.7719 (tpt170) REVERT: E 183 ARG cc_start: 0.7508 (tpp80) cc_final: 0.6780 (tpt170) REVERT: F 485 GLN cc_start: 0.8905 (mt0) cc_final: 0.8657 (mt0) REVERT: G 233 ARG cc_start: 0.8095 (tpt170) cc_final: 0.7867 (tpt170) REVERT: G 240 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7479 (ttp-110) REVERT: I 243 LYS cc_start: 0.8461 (tppt) cc_final: 0.7914 (mmtt) REVERT: I 283 ARG cc_start: 0.7976 (tpt90) cc_final: 0.7462 (tpp80) REVERT: K 190 ARG cc_start: 0.7198 (mpp80) cc_final: 0.6854 (mmt180) REVERT: K 233 ARG cc_start: 0.8158 (tpt170) cc_final: 0.7944 (tpt170) REVERT: K 283 ARG cc_start: 0.7899 (tpt90) cc_final: 0.7373 (tpp80) REVERT: K 287 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7864 (mm-30) REVERT: M 190 ARG cc_start: 0.7443 (mtm110) cc_final: 0.7104 (mtm110) REVERT: M 283 ARG cc_start: 0.7707 (tpt90) cc_final: 0.7254 (tpp80) REVERT: O 190 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6614 (mtm110) REVERT: O 283 ARG cc_start: 0.7938 (tpt90) cc_final: 0.7529 (tpt170) REVERT: O 340 ARG cc_start: 0.8311 (mtm110) cc_final: 0.8067 (mtm110) REVERT: Q 183 ARG cc_start: 0.7484 (tpp80) cc_final: 0.6974 (tpt90) REVERT: Q 240 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7682 (ttp80) REVERT: R 485 GLN cc_start: 0.8886 (mt0) cc_final: 0.8598 (mt0) REVERT: S 283 ARG cc_start: 0.7955 (tpt90) cc_final: 0.7492 (tpt170) REVERT: T 475 MET cc_start: 0.8292 (mmm) cc_final: 0.7868 (mmm) REVERT: V 523 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6577 (ptpp) REVERT: W 183 ARG cc_start: 0.7354 (tpp80) cc_final: 0.6766 (tpt-90) REVERT: W 378 MET cc_start: 0.7672 (tpt) cc_final: 0.6880 (mtt) outliers start: 22 outliers final: 18 residues processed: 394 average time/residue: 0.4096 time to fit residues: 233.6363 Evaluate side-chains 377 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 358 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain H residue 491 ASP Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain V residue 486 MET Chi-restraints excluded: chain V residue 523 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 112 optimal weight: 20.0000 chunk 239 optimal weight: 0.6980 chunk 500 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 483 optimal weight: 6.9990 chunk 269 optimal weight: 50.0000 chunk 360 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 chunk 9 optimal weight: 40.0000 chunk 125 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.247127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.194507 restraints weight = 44210.798| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.22 r_work: 0.3587 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43692 Z= 0.123 Angle : 0.375 9.872 58176 Z= 0.201 Chirality : 0.032 0.142 7980 Planarity : 0.002 0.025 6396 Dihedral : 2.516 30.521 6806 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.69 % Allowed : 5.36 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.38 (0.09), residues: 6252 helix: 4.28 (0.05), residues: 5928 sheet: None (None), residues: 0 loop : 0.44 (0.19), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 240 TYR 0.022 0.002 TYR T 517 PHE 0.007 0.001 PHE Q 435 HIS 0.004 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00294 (43692) covalent geometry : angle 0.37494 (58176) hydrogen bonds : bond 0.04301 ( 3917) hydrogen bonds : angle 2.89168 (11751) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 379 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8041 (tpt170) cc_final: 0.7736 (tpt170) REVERT: A 283 ARG cc_start: 0.7776 (tpt90) cc_final: 0.7293 (tpp80) REVERT: A 378 MET cc_start: 0.7577 (tpt) cc_final: 0.6930 (mtt) REVERT: A 442 LEU cc_start: 0.8637 (mt) cc_final: 0.8426 (mp) REVERT: C 138 VAL cc_start: 0.6491 (t) cc_final: 0.6281 (t) REVERT: C 183 ARG cc_start: 0.7167 (tpt90) cc_final: 0.6967 (mmm-85) REVERT: C 243 LYS cc_start: 0.8305 (tppp) cc_final: 0.7636 (mmtt) REVERT: C 283 ARG cc_start: 0.7947 (tpt90) cc_final: 0.7596 (tpt170) REVERT: E 183 ARG cc_start: 0.7268 (tpp80) cc_final: 0.6583 (tpt170) REVERT: F 485 GLN cc_start: 0.8833 (mt0) cc_final: 0.8589 (mt0) REVERT: G 233 ARG cc_start: 0.8053 (tpt170) cc_final: 0.7837 (tpt170) REVERT: G 240 ARG cc_start: 0.7851 (ttp-110) cc_final: 0.7354 (ttp-110) REVERT: I 183 ARG cc_start: 0.7230 (mmm-85) cc_final: 0.6334 (tpt170) REVERT: I 243 LYS cc_start: 0.8339 (tppt) cc_final: 0.7785 (mmtt) REVERT: I 283 ARG cc_start: 0.7816 (tpt90) cc_final: 0.7286 (tpp80) REVERT: K 190 ARG cc_start: 0.7145 (mpp80) cc_final: 0.6872 (mmt180) REVERT: K 233 ARG cc_start: 0.8085 (tpt170) cc_final: 0.7823 (tpt170) REVERT: K 283 ARG cc_start: 0.7799 (tpt90) cc_final: 0.7263 (tpp80) REVERT: K 287 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7813 (mm-30) REVERT: M 190 ARG cc_start: 0.7340 (mtm110) cc_final: 0.6926 (mtm110) REVERT: M 258 ARG cc_start: 0.7626 (tpp80) cc_final: 0.7024 (tpp80) REVERT: M 283 ARG cc_start: 0.7552 (tpt90) cc_final: 0.7134 (tpp80) REVERT: M 336 ASN cc_start: 0.8782 (t0) cc_final: 0.8400 (t0) REVERT: O 283 ARG cc_start: 0.7776 (tpt90) cc_final: 0.7368 (tpt170) REVERT: O 378 MET cc_start: 0.7628 (tpt) cc_final: 0.6984 (mtt) REVERT: Q 183 ARG cc_start: 0.7164 (tpp80) cc_final: 0.6580 (tpt90) REVERT: Q 240 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7594 (ttp80) REVERT: Q 308 MET cc_start: 0.8422 (mtp) cc_final: 0.8046 (mtp) REVERT: R 485 GLN cc_start: 0.8732 (mt0) cc_final: 0.8343 (mt0) REVERT: S 283 ARG cc_start: 0.7889 (tpt90) cc_final: 0.7394 (tpt170) REVERT: S 449 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.8083 (ttm170) REVERT: U 340 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7888 (mtm110) REVERT: V 485 GLN cc_start: 0.8754 (mt0) cc_final: 0.8542 (mt0) REVERT: V 523 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6596 (ptpp) REVERT: W 378 MET cc_start: 0.7495 (tpt) cc_final: 0.6681 (mtt) outliers start: 29 outliers final: 19 residues processed: 399 average time/residue: 0.3932 time to fit residues: 228.7392 Evaluate side-chains 386 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 366 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain H residue 491 ASP Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain V residue 523 LYS Chi-restraints excluded: chain W residue 451 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 453 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 337 optimal weight: 0.7980 chunk 201 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 chunk 501 optimal weight: 0.7980 chunk 581 optimal weight: 50.0000 chunk 346 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.246558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.195747 restraints weight = 44448.148| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.32 r_work: 0.3604 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 0.069 43692 Z= 0.139 Angle : 0.398 8.946 58176 Z= 0.211 Chirality : 0.033 0.166 7980 Planarity : 0.002 0.034 6396 Dihedral : 2.531 30.610 6806 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.89 % Allowed : 5.65 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.35 (0.09), residues: 6252 helix: 4.25 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.44 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG U 190 TYR 0.022 0.002 TYR V 517 PHE 0.009 0.001 PHE Q 435 HIS 0.004 0.002 HIS E 422 Details of bonding type rmsd covalent geometry : bond 0.00348 (43692) covalent geometry : angle 0.39823 (58176) hydrogen bonds : bond 0.04484 ( 3917) hydrogen bonds : angle 2.91426 (11751) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 373 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7102 (tpp80) cc_final: 0.6410 (tpt170) REVERT: A 190 ARG cc_start: 0.7120 (mtm110) cc_final: 0.6650 (mtm110) REVERT: A 233 ARG cc_start: 0.8017 (tpt170) cc_final: 0.7713 (tpt170) REVERT: A 283 ARG cc_start: 0.7739 (tpt90) cc_final: 0.7256 (tpp80) REVERT: A 442 LEU cc_start: 0.8662 (mt) cc_final: 0.8441 (mp) REVERT: C 183 ARG cc_start: 0.7215 (tpt90) cc_final: 0.7001 (mmm-85) REVERT: C 243 LYS cc_start: 0.8330 (tppp) cc_final: 0.7684 (mmtt) REVERT: C 283 ARG cc_start: 0.7899 (tpt90) cc_final: 0.7548 (tpt170) REVERT: E 183 ARG cc_start: 0.7268 (tpp80) cc_final: 0.6653 (tpt170) REVERT: F 485 GLN cc_start: 0.8852 (mt0) cc_final: 0.8599 (mt0) REVERT: G 233 ARG cc_start: 0.8029 (tpt170) cc_final: 0.7813 (tpt170) REVERT: G 240 ARG cc_start: 0.7778 (ttp-110) cc_final: 0.7464 (ttp-110) REVERT: I 190 ARG cc_start: 0.7414 (mtm110) cc_final: 0.6593 (mtm110) REVERT: I 243 LYS cc_start: 0.8283 (tppt) cc_final: 0.7793 (tptp) REVERT: I 283 ARG cc_start: 0.7807 (tpt90) cc_final: 0.7305 (tpp80) REVERT: K 190 ARG cc_start: 0.7176 (mpp80) cc_final: 0.6911 (mmt180) REVERT: K 233 ARG cc_start: 0.8036 (tpt170) cc_final: 0.7824 (tpt170) REVERT: K 283 ARG cc_start: 0.7755 (tpt90) cc_final: 0.7243 (tpp80) REVERT: K 287 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7731 (mm-30) REVERT: M 190 ARG cc_start: 0.7345 (mtm110) cc_final: 0.6931 (mtm110) REVERT: M 258 ARG cc_start: 0.7537 (tpp80) cc_final: 0.6949 (tpp80) REVERT: M 283 ARG cc_start: 0.7541 (tpt90) cc_final: 0.7132 (tpp80) REVERT: M 336 ASN cc_start: 0.8775 (t0) cc_final: 0.8458 (t0) REVERT: M 408 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7671 (mm-30) REVERT: O 283 ARG cc_start: 0.7685 (tpt90) cc_final: 0.7278 (tpt170) REVERT: O 378 MET cc_start: 0.7643 (tpt) cc_final: 0.6999 (mtt) REVERT: Q 183 ARG cc_start: 0.7292 (tpp80) cc_final: 0.6804 (tpt90) REVERT: Q 240 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7506 (ttp80) REVERT: Q 308 MET cc_start: 0.8435 (mtp) cc_final: 0.8037 (mtp) REVERT: R 485 GLN cc_start: 0.8761 (mt0) cc_final: 0.8364 (mt0) REVERT: S 283 ARG cc_start: 0.7834 (tpt90) cc_final: 0.7178 (tpt170) REVERT: S 287 GLU cc_start: 0.8110 (tp30) cc_final: 0.7549 (tp30) REVERT: U 190 ARG cc_start: 0.7481 (mtm110) cc_final: 0.7003 (mtm110) REVERT: U 340 ARG cc_start: 0.8028 (mtm110) cc_final: 0.7798 (mtm110) REVERT: V 485 GLN cc_start: 0.8793 (mt0) cc_final: 0.8564 (mt0) REVERT: V 523 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6614 (ptpp) REVERT: W 183 ARG cc_start: 0.7232 (tpp80) cc_final: 0.6598 (tpt170) REVERT: W 378 MET cc_start: 0.7538 (tpt) cc_final: 0.6720 (mtt) outliers start: 37 outliers final: 28 residues processed: 402 average time/residue: 0.4054 time to fit residues: 235.8993 Evaluate side-chains 385 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 356 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain J residue 486 MET Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 491 ASP Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain V residue 523 LYS Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 504 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 282 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 246 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 242 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 566 optimal weight: 1.9990 chunk 426 optimal weight: 80.0000 chunk 356 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 336 ASN ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 525 GLN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 525 GLN ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 429 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.249790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.199454 restraints weight = 44169.706| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.33 r_work: 0.3592 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 43692 Z= 0.101 Angle : 0.354 8.910 58176 Z= 0.191 Chirality : 0.032 0.138 7980 Planarity : 0.002 0.051 6396 Dihedral : 2.417 22.441 6806 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.77 % Allowed : 6.13 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.71 (0.09), residues: 6252 helix: 4.49 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.35 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 190 TYR 0.020 0.002 TYR V 517 PHE 0.005 0.001 PHE Q 435 HIS 0.004 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00227 (43692) covalent geometry : angle 0.35401 (58176) hydrogen bonds : bond 0.03771 ( 3917) hydrogen bonds : angle 2.73410 (11751) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 385 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 MET cc_start: 0.7562 (tpt) cc_final: 0.6835 (mtt) REVERT: A 442 LEU cc_start: 0.8618 (mt) cc_final: 0.8412 (mp) REVERT: C 183 ARG cc_start: 0.7147 (tpt90) cc_final: 0.6891 (mmm-85) REVERT: C 233 ARG cc_start: 0.7872 (tpt170) cc_final: 0.7654 (tpp-160) REVERT: C 240 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7244 (ttp80) REVERT: C 243 LYS cc_start: 0.8320 (tppp) cc_final: 0.7710 (mmtt) REVERT: C 283 ARG cc_start: 0.7921 (tpt90) cc_final: 0.7481 (tpt170) REVERT: C 287 GLU cc_start: 0.8190 (tp30) cc_final: 0.7816 (tp30) REVERT: E 183 ARG cc_start: 0.7235 (tpp80) cc_final: 0.6573 (tpt170) REVERT: F 485 GLN cc_start: 0.8729 (mt0) cc_final: 0.8468 (mt0) REVERT: G 244 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7981 (mt-10) REVERT: I 183 ARG cc_start: 0.7274 (mmm-85) cc_final: 0.6411 (tpt170) REVERT: I 190 ARG cc_start: 0.7299 (mtm110) cc_final: 0.6900 (mtm110) REVERT: I 243 LYS cc_start: 0.8234 (tppt) cc_final: 0.7735 (tptp) REVERT: I 283 ARG cc_start: 0.7779 (tpt90) cc_final: 0.7281 (tpp80) REVERT: I 287 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7619 (mm-30) REVERT: K 190 ARG cc_start: 0.7103 (mpp80) cc_final: 0.6853 (mmt180) REVERT: K 233 ARG cc_start: 0.7885 (tpt170) cc_final: 0.7616 (tpt170) REVERT: K 283 ARG cc_start: 0.7778 (tpt90) cc_final: 0.7196 (tpp80) REVERT: K 287 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7696 (mm-30) REVERT: L 475 MET cc_start: 0.8239 (mmt) cc_final: 0.8035 (mmm) REVERT: M 336 ASN cc_start: 0.8772 (t0) cc_final: 0.8328 (t0) REVERT: O 183 ARG cc_start: 0.7294 (mmm-85) cc_final: 0.6548 (tpt170) REVERT: O 283 ARG cc_start: 0.7697 (tpt90) cc_final: 0.7290 (tpt170) REVERT: O 378 MET cc_start: 0.7626 (tpt) cc_final: 0.6961 (mtt) REVERT: Q 240 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7402 (ttp80) REVERT: Q 308 MET cc_start: 0.8401 (mtp) cc_final: 0.8032 (mtp) REVERT: R 485 GLN cc_start: 0.8665 (mt0) cc_final: 0.8412 (mt0) REVERT: S 244 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7827 (mt-10) REVERT: S 287 GLU cc_start: 0.8231 (tp30) cc_final: 0.7838 (mm-30) REVERT: T 485 GLN cc_start: 0.8848 (mt0) cc_final: 0.8600 (mt0) REVERT: U 183 ARG cc_start: 0.7240 (tpt170) cc_final: 0.6745 (tpp80) REVERT: U 340 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7965 (mtm110) REVERT: V 523 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6608 (ptpp) REVERT: W 183 ARG cc_start: 0.7156 (tpp80) cc_final: 0.6525 (tpt170) REVERT: W 378 MET cc_start: 0.7410 (tpt) cc_final: 0.6641 (mtt) outliers start: 32 outliers final: 22 residues processed: 408 average time/residue: 0.3631 time to fit residues: 220.5104 Evaluate side-chains 385 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 362 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain H residue 491 ASP Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain L residue 486 MET Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain U residue 451 ILE Chi-restraints excluded: chain V residue 523 LYS Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 504 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 177 optimal weight: 5.9990 chunk 486 optimal weight: 4.9990 chunk 378 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 388 optimal weight: 3.9990 chunk 519 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 366 optimal weight: 50.0000 chunk 610 optimal weight: 2.9990 chunk 219 optimal weight: 50.0000 chunk 88 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 422 HIS ** O 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.241260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.189078 restraints weight = 44351.777| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.21 r_work: 0.3542 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 43692 Z= 0.299 Angle : 0.599 11.089 58176 Z= 0.303 Chirality : 0.039 0.262 7980 Planarity : 0.003 0.042 6396 Dihedral : 2.838 26.905 6804 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.13 % Allowed : 6.47 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.41 (0.09), residues: 6252 helix: 3.67 (0.06), residues: 5916 sheet: None (None), residues: 0 loop : 0.23 (0.21), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 190 TYR 0.022 0.003 TYR V 517 PHE 0.016 0.003 PHE S 435 HIS 0.004 0.001 HIS W 429 Details of bonding type rmsd covalent geometry : bond 0.00803 (43692) covalent geometry : angle 0.59884 (58176) hydrogen bonds : bond 0.06056 ( 3917) hydrogen bonds : angle 3.27927 (11751) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 385 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.7996 (tpt170) cc_final: 0.7690 (tpt170) REVERT: A 283 ARG cc_start: 0.7712 (tpt90) cc_final: 0.7181 (tpp80) REVERT: A 442 LEU cc_start: 0.8705 (mt) cc_final: 0.8491 (mp) REVERT: C 183 ARG cc_start: 0.7340 (tpt90) cc_final: 0.7120 (mmm-85) REVERT: C 283 ARG cc_start: 0.7916 (tpt90) cc_final: 0.7523 (tpt170) REVERT: E 144 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7697 (mt-10) REVERT: E 337 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7621 (mm-30) REVERT: E 409 GLU cc_start: 0.7526 (tp30) cc_final: 0.7278 (tp30) REVERT: I 190 ARG cc_start: 0.7398 (mtm110) cc_final: 0.6898 (mtm110) REVERT: I 283 ARG cc_start: 0.7897 (tpt90) cc_final: 0.7419 (tpp80) REVERT: I 287 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7591 (mm-30) REVERT: K 190 ARG cc_start: 0.7116 (mpp80) cc_final: 0.6849 (mmt180) REVERT: K 233 ARG cc_start: 0.8058 (tpt170) cc_final: 0.7819 (tpt170) REVERT: K 283 ARG cc_start: 0.7912 (tpt90) cc_final: 0.7333 (tpp80) REVERT: K 287 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7825 (mm-30) REVERT: M 159 ILE cc_start: 0.5726 (mt) cc_final: 0.5483 (mp) REVERT: M 258 ARG cc_start: 0.7747 (tpp80) cc_final: 0.7045 (tpp80) REVERT: M 283 ARG cc_start: 0.7658 (tpt90) cc_final: 0.7212 (tpp80) REVERT: O 283 ARG cc_start: 0.7766 (tpt90) cc_final: 0.7228 (tpt170) REVERT: O 287 GLU cc_start: 0.8092 (tp30) cc_final: 0.7643 (tp30) REVERT: Q 183 ARG cc_start: 0.7462 (tpp80) cc_final: 0.6785 (tpt170) REVERT: Q 240 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7345 (ttp80) REVERT: R 485 GLN cc_start: 0.8932 (mt0) cc_final: 0.8647 (mt0) REVERT: S 194 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6920 (mm-30) REVERT: S 283 ARG cc_start: 0.7887 (tpt90) cc_final: 0.7555 (tpt170) REVERT: V 523 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6519 (ptpp) REVERT: W 183 ARG cc_start: 0.7430 (tpp80) cc_final: 0.6734 (tpt170) REVERT: W 378 MET cc_start: 0.7751 (tpt) cc_final: 0.7009 (mtt) outliers start: 47 outliers final: 39 residues processed: 422 average time/residue: 0.3887 time to fit residues: 238.7059 Evaluate side-chains 404 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 364 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain F residue 491 ASP Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain H residue 491 ASP Chi-restraints excluded: chain H residue 518 LEU Chi-restraints excluded: chain I residue 293 LYS Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain L residue 491 ASP Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain N residue 491 ASP Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain P residue 491 ASP Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain T residue 491 ASP Chi-restraints excluded: chain U residue 451 ILE Chi-restraints excluded: chain V residue 523 LYS Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 504 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 191 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 440 optimal weight: 0.6980 chunk 477 optimal weight: 40.0000 chunk 306 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 50.0000 chunk 402 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 336 ASN ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.247887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.197349 restraints weight = 43888.098| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.06 r_work: 0.3656 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 43692 Z= 0.115 Angle : 0.393 10.019 58176 Z= 0.210 Chirality : 0.032 0.146 7980 Planarity : 0.002 0.034 6396 Dihedral : 2.516 18.494 6804 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.79 % Allowed : 6.80 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.30 (0.09), residues: 6252 helix: 4.22 (0.06), residues: 5940 sheet: None (None), residues: 0 loop : 0.48 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 340 TYR 0.019 0.002 TYR V 517 PHE 0.007 0.001 PHE U 435 HIS 0.004 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00267 (43692) covalent geometry : angle 0.39340 (58176) hydrogen bonds : bond 0.04147 ( 3917) hydrogen bonds : angle 2.86725 (11751) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 358 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7163 (tpp80) cc_final: 0.6486 (tpt170) REVERT: A 442 LEU cc_start: 0.8628 (mt) cc_final: 0.8407 (mp) REVERT: C 183 ARG cc_start: 0.7206 (tpt90) cc_final: 0.6996 (mmm-85) REVERT: C 243 LYS cc_start: 0.8278 (tppp) cc_final: 0.7618 (mmtt) REVERT: C 283 ARG cc_start: 0.7885 (tpt90) cc_final: 0.7417 (tpp80) REVERT: F 485 GLN cc_start: 0.8803 (mt0) cc_final: 0.8535 (mt0) REVERT: G 244 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8023 (mt-10) REVERT: I 183 ARG cc_start: 0.7315 (mmm-85) cc_final: 0.6418 (tpt170) REVERT: I 190 ARG cc_start: 0.7424 (mtm110) cc_final: 0.6994 (mtm110) REVERT: I 243 LYS cc_start: 0.8305 (tppp) cc_final: 0.7747 (mmtt) REVERT: I 283 ARG cc_start: 0.7799 (tpt90) cc_final: 0.7339 (tpp80) REVERT: I 287 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7516 (mm-30) REVERT: K 190 ARG cc_start: 0.7156 (mpp80) cc_final: 0.6934 (mmt180) REVERT: K 233 ARG cc_start: 0.7986 (tpt170) cc_final: 0.7748 (tpt170) REVERT: K 283 ARG cc_start: 0.7722 (tpt90) cc_final: 0.7216 (tpp80) REVERT: K 287 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7753 (mm-30) REVERT: M 258 ARG cc_start: 0.7481 (tpp80) cc_final: 0.6862 (tpp80) REVERT: M 336 ASN cc_start: 0.8751 (t0) cc_final: 0.8378 (t0) REVERT: O 183 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.6630 (tpt170) REVERT: O 240 ARG cc_start: 0.6925 (ttp80) cc_final: 0.6687 (ttp-110) REVERT: O 283 ARG cc_start: 0.7683 (tpt90) cc_final: 0.7303 (tpt170) REVERT: O 378 MET cc_start: 0.7587 (tpt) cc_final: 0.6964 (mtt) REVERT: P 511 LEU cc_start: 0.7647 (mm) cc_final: 0.7357 (mt) REVERT: Q 183 ARG cc_start: 0.7263 (tpp80) cc_final: 0.6648 (tpt170) REVERT: Q 240 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7386 (ttp80) REVERT: R 485 GLN cc_start: 0.8699 (mt0) cc_final: 0.8478 (mt0) REVERT: S 194 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6927 (mm-30) REVERT: S 244 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7833 (mt-10) REVERT: S 287 GLU cc_start: 0.8066 (tp30) cc_final: 0.7820 (mm-30) REVERT: T 485 GLN cc_start: 0.8798 (mt0) cc_final: 0.8550 (mt0) REVERT: V 523 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6440 (ptpp) REVERT: W 378 MET cc_start: 0.7430 (tpt) cc_final: 0.6665 (mtt) outliers start: 33 outliers final: 30 residues processed: 385 average time/residue: 0.3765 time to fit residues: 213.2099 Evaluate side-chains 377 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 346 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain H residue 491 ASP Chi-restraints excluded: chain H residue 518 LEU Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain N residue 491 ASP Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain U residue 451 ILE Chi-restraints excluded: chain V residue 523 LYS Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 504 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 430 optimal weight: 7.9990 chunk 215 optimal weight: 40.0000 chunk 467 optimal weight: 6.9990 chunk 296 optimal weight: 0.9990 chunk 520 optimal weight: 110.0000 chunk 72 optimal weight: 0.7980 chunk 315 optimal weight: 0.3980 chunk 234 optimal weight: 0.8980 chunk 507 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 247 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 GLN ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 525 GLN ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 525 GLN O 336 ASN ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 525 GLN ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 525 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.249041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.196764 restraints weight = 44262.038| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.22 r_work: 0.3564 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 43692 Z= 0.110 Angle : 0.385 9.951 58176 Z= 0.207 Chirality : 0.032 0.168 7980 Planarity : 0.002 0.036 6396 Dihedral : 2.443 20.341 6804 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.62 % Allowed : 7.11 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.58 (0.09), residues: 6252 helix: 4.40 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.44 (0.22), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 190 TYR 0.018 0.002 TYR V 517 PHE 0.006 0.001 PHE S 435 HIS 0.004 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00257 (43692) covalent geometry : angle 0.38462 (58176) hydrogen bonds : bond 0.03895 ( 3917) hydrogen bonds : angle 2.78914 (11751) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 356 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7067 (tpp80) cc_final: 0.6298 (tpt170) REVERT: A 190 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6804 (mtm110) REVERT: A 378 MET cc_start: 0.7627 (tpt) cc_final: 0.6828 (mtt) REVERT: C 183 ARG cc_start: 0.7180 (tpt90) cc_final: 0.6918 (mmm-85) REVERT: C 243 LYS cc_start: 0.8264 (tppp) cc_final: 0.7593 (mmtt) REVERT: C 283 ARG cc_start: 0.7801 (tpt90) cc_final: 0.7277 (tpp80) REVERT: E 258 ARG cc_start: 0.7981 (tpt90) cc_final: 0.7702 (tpt90) REVERT: F 485 GLN cc_start: 0.8741 (mt0) cc_final: 0.8452 (mt0) REVERT: H 479 LEU cc_start: 0.8638 (tt) cc_final: 0.8398 (tp) REVERT: I 183 ARG cc_start: 0.7270 (mmm-85) cc_final: 0.6291 (tpt170) REVERT: I 190 ARG cc_start: 0.7307 (mtm110) cc_final: 0.6812 (mtm110) REVERT: I 243 LYS cc_start: 0.8316 (tppp) cc_final: 0.7741 (mmtt) REVERT: I 283 ARG cc_start: 0.7779 (tpt90) cc_final: 0.7263 (tpp80) REVERT: I 287 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7594 (mm-30) REVERT: K 190 ARG cc_start: 0.7104 (mpp80) cc_final: 0.6845 (mmt180) REVERT: K 233 ARG cc_start: 0.7892 (tpt170) cc_final: 0.7601 (tpt170) REVERT: K 283 ARG cc_start: 0.7757 (tpt90) cc_final: 0.7158 (tpp80) REVERT: K 287 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7713 (mm-30) REVERT: K 340 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7846 (mtm110) REVERT: L 475 MET cc_start: 0.8249 (mmt) cc_final: 0.8045 (mmm) REVERT: M 183 ARG cc_start: 0.6992 (tpt170) cc_final: 0.6775 (tpp80) REVERT: M 336 ASN cc_start: 0.8748 (t0) cc_final: 0.8318 (t0) REVERT: O 183 ARG cc_start: 0.7308 (mmm-85) cc_final: 0.6517 (tpt170) REVERT: O 283 ARG cc_start: 0.7639 (tpt90) cc_final: 0.7157 (tpt170) REVERT: O 287 GLU cc_start: 0.8017 (tp30) cc_final: 0.7604 (tp30) REVERT: O 336 ASN cc_start: 0.8528 (t0) cc_final: 0.8230 (t0) REVERT: O 340 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7829 (mtm110) REVERT: O 378 MET cc_start: 0.7664 (tpt) cc_final: 0.6951 (mtt) REVERT: P 511 LEU cc_start: 0.7497 (mm) cc_final: 0.7220 (mt) REVERT: Q 183 ARG cc_start: 0.7272 (tpp80) cc_final: 0.6571 (tpt170) REVERT: Q 240 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7246 (ttp80) REVERT: R 485 GLN cc_start: 0.8673 (mt0) cc_final: 0.8432 (mt0) REVERT: S 194 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7138 (mm-30) REVERT: S 244 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7889 (mt-10) REVERT: S 250 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8276 (mt) REVERT: S 287 GLU cc_start: 0.8195 (tp30) cc_final: 0.7795 (mm-30) REVERT: T 485 GLN cc_start: 0.8826 (mt0) cc_final: 0.8569 (mt0) REVERT: U 183 ARG cc_start: 0.7212 (tpt170) cc_final: 0.6728 (tpp80) REVERT: V 523 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6443 (ptpp) REVERT: W 183 ARG cc_start: 0.7125 (tpp80) cc_final: 0.6344 (tpt170) REVERT: W 378 MET cc_start: 0.7502 (tpt) cc_final: 0.6656 (mtt) outliers start: 26 outliers final: 21 residues processed: 376 average time/residue: 0.3685 time to fit residues: 205.5242 Evaluate side-chains 372 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 349 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 250 ILE Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain U residue 451 ILE Chi-restraints excluded: chain V residue 523 LYS Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 504 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 337 optimal weight: 0.9980 chunk 282 optimal weight: 6.9990 chunk 475 optimal weight: 50.0000 chunk 512 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 515 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 405 optimal weight: 0.9990 chunk 581 optimal weight: 50.0000 chunk 128 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.246796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.195572 restraints weight = 44392.382| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.31 r_work: 0.3618 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 43692 Z= 0.138 Angle : 0.417 10.040 58176 Z= 0.221 Chirality : 0.033 0.177 7980 Planarity : 0.002 0.040 6396 Dihedral : 2.499 20.124 6804 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.77 % Allowed : 7.28 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.45 (0.09), residues: 6252 helix: 4.32 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.40 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG U 190 TYR 0.018 0.002 TYR B 517 PHE 0.010 0.001 PHE Q 435 HIS 0.004 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00346 (43692) covalent geometry : angle 0.41727 (58176) hydrogen bonds : bond 0.04343 ( 3917) hydrogen bonds : angle 2.87009 (11751) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10193.58 seconds wall clock time: 175 minutes 57.27 seconds (10557.27 seconds total)