Starting phenix.real_space_refine on Thu Dec 26 03:35:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cwy_27031/12_2024/8cwy_27031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cwy_27031/12_2024/8cwy_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_27031/12_2024/8cwy_27031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cwy_27031/12_2024/8cwy_27031.map" model { file = "/net/cci-nas-00/data/ceres_data/8cwy_27031/12_2024/8cwy_27031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cwy_27031/12_2024/8cwy_27031.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: {'TYR:plan': 2, 'GLU:plan': 26, 'ARG:plan': 12, 'ASP:plan': 3} 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: 24.50, per 1000 atoms: 0.56 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: 11.96 Conformation dependent library (CDL) restraints added in 6.4 seconds 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: 3.98 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: 15.64 Time building geometry restraints manager: 13.48 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: 0.00 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.860 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 93.090 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.340 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.120 ------------------------------------------------------------------------------- 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= 0.162 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.001 0.000 HIS A 429 PHE 0.009 0.001 PHE O 435 TYR 0.003 0.001 TYR D 517 ARG 0.002 0.000 ARG A 343 *********************** 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 : 5.563 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: 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: 0.7158 (tpt170) REVERT: D 475 MET cc_start: 0.8018 (tpp) cc_final: 0.7206 (tpt) REVERT: E 449 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7705 (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: 0.6502 (tpt170) REVERT: I 378 MET cc_start: 0.6544 (tpt) cc_final: 0.6013 (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: 0.7023 (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: 0.7056 (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: 0.6968 (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: 0.8774 time to fit residues: 630.7193 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 : 4.912 ------------------------------------------------------------------------------- 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 526 optimal weight: 40.0000 chunk 472 optimal weight: 6.9990 chunk 262 optimal weight: 40.0000 chunk 161 optimal weight: 40.0000 chunk 319 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 489 optimal weight: 10.0000 chunk 189 optimal weight: 0.7980 chunk 297 optimal weight: 0.8980 chunk 364 optimal weight: 100.0000 chunk 566 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.1575 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= 0.295 Angle : 0.458 6.144 58176 Z= 0.237 Chirality : 0.034 0.123 7980 Planarity : 0.003 0.048 6396 Dihedral : 2.598 34.305 6806 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.38 % Allowed : 3.30 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.15 (0.09), residues: 6252 helix: 4.12 (0.06), residues: 5892 sheet: None (None), residues: 0 loop : 1.15 (0.23), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.007 0.002 PHE Q 435 TYR 0.022 0.002 TYR P 517 ARG 0.010 0.001 ARG K 190 *********************** 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 421 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 405 time to evaluate : 5.042 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 442 LEU cc_start: 0.8665 (mt) cc_final: 0.8463 (mp) REVERT: C 243 LYS cc_start: 0.7913 (tppp) cc_final: 0.7493 (mmtt) REVERT: C 283 ARG cc_start: 0.7416 (tpt90) cc_final: 0.6793 (tpt170) REVERT: F 485 GLN cc_start: 0.8756 (mt0) cc_final: 0.8470 (mt0) REVERT: I 378 MET cc_start: 0.6569 (tpt) cc_final: 0.6115 (tpt) REVERT: O 283 ARG cc_start: 0.7504 (tpt90) cc_final: 0.7104 (tpt170) REVERT: R 485 GLN cc_start: 0.8645 (mt0) cc_final: 0.8381 (mt0) REVERT: S 283 ARG cc_start: 0.7399 (tpt90) cc_final: 0.7042 (tpt170) REVERT: S 449 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8115 (ttm170) REVERT: T 475 MET cc_start: 0.7688 (mmm) cc_final: 0.7248 (mmm) outliers start: 16 outliers final: 8 residues processed: 412 average time/residue: 0.8052 time to fit residues: 483.4801 Evaluate side-chains 368 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 360 time to evaluate : 5.152 ------------------------------------------------------------------------------- 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 314 optimal weight: 50.0000 chunk 175 optimal weight: 8.9990 chunk 471 optimal weight: 40.0000 chunk 385 optimal weight: 0.7980 chunk 156 optimal weight: 80.0000 chunk 567 optimal weight: 0.9980 chunk 613 optimal weight: 3.9990 chunk 505 optimal weight: 0.7980 chunk 562 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 455 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43692 Z= 0.186 Angle : 0.381 9.573 58176 Z= 0.202 Chirality : 0.032 0.107 7980 Planarity : 0.002 0.036 6396 Dihedral : 2.472 27.459 6806 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.74 % Allowed : 3.74 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.53 (0.09), residues: 6252 helix: 4.35 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.90 (0.22), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.005 0.001 PHE Q 435 TYR 0.022 0.002 TYR V 517 ARG 0.007 0.000 ARG I 133 *********************** 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 429 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 398 time to evaluate : 5.511 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: C 243 LYS cc_start: 0.7953 (tppp) cc_final: 0.7567 (mmtt) REVERT: F 485 GLN cc_start: 0.8665 (mt0) cc_final: 0.8355 (mt0) REVERT: I 378 MET cc_start: 0.6358 (tpt) cc_final: 0.5905 (tpt) REVERT: M 336 ASN cc_start: 0.8539 (t0) cc_final: 0.8142 (t0) REVERT: O 283 ARG cc_start: 0.7416 (tpt90) cc_final: 0.7036 (tpt170) REVERT: R 485 GLN cc_start: 0.8529 (mt0) cc_final: 0.8186 (mt0) REVERT: S 449 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.8012 (ttm170) REVERT: T 485 GLN cc_start: 0.8623 (mt0) cc_final: 0.8339 (mt0) outliers start: 31 outliers final: 15 residues processed: 419 average time/residue: 0.7505 time to fit residues: 469.1052 Evaluate side-chains 367 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 352 time to evaluate : 5.252 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 3.9990 chunk 426 optimal weight: 80.0000 chunk 294 optimal weight: 4.9990 chunk 62 optimal weight: 50.0000 chunk 270 optimal weight: 90.0000 chunk 381 optimal weight: 5.9990 chunk 569 optimal weight: 1.9990 chunk 603 optimal weight: 0.6980 chunk 297 optimal weight: 0.0170 chunk 539 optimal weight: 9.9990 chunk 162 optimal weight: 0.1980 overall best weight: 1.3822 ------------------------------------------------------------------------------- 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 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 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 336 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 43692 Z= 0.227 Angle : 0.396 9.369 58176 Z= 0.208 Chirality : 0.033 0.157 7980 Planarity : 0.002 0.027 6396 Dihedral : 2.480 18.388 6804 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.53 % Allowed : 4.50 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.50 (0.09), residues: 6252 helix: 4.34 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.69 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.009 0.001 PHE Q 435 TYR 0.023 0.002 TYR P 517 ARG 0.006 0.000 ARG C 183 *********************** 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 404 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 382 time to evaluate : 4.992 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: C 243 LYS cc_start: 0.7981 (tppp) cc_final: 0.7609 (mmtt) REVERT: F 485 GLN cc_start: 0.8722 (mt0) cc_final: 0.8439 (mt0) REVERT: M 336 ASN cc_start: 0.8583 (t0) cc_final: 0.8276 (t0) REVERT: O 283 ARG cc_start: 0.7389 (tpt90) cc_final: 0.7016 (tpt170) REVERT: R 485 GLN cc_start: 0.8595 (mt0) cc_final: 0.8235 (mt0) REVERT: S 449 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.7991 (ttm170) outliers start: 22 outliers final: 17 residues processed: 392 average time/residue: 0.8227 time to fit residues: 474.3327 Evaluate side-chains 380 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 363 time to evaluate : 5.293 ------------------------------------------------------------------------------- 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 I residue 345 SER Chi-restraints excluded: chain J residue 486 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 2.9990 chunk 342 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 449 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 514 optimal weight: 9.9990 chunk 416 optimal weight: 70.0000 chunk 0 optimal weight: 120.0000 chunk 307 optimal weight: 2.9990 chunk 541 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 43692 Z= 0.262 Angle : 0.414 9.248 58176 Z= 0.215 Chirality : 0.033 0.164 7980 Planarity : 0.002 0.037 6396 Dihedral : 2.515 19.198 6804 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.60 % Allowed : 5.51 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.38 (0.09), residues: 6252 helix: 4.27 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.55 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.010 0.002 PHE Q 435 TYR 0.022 0.002 TYR T 517 ARG 0.008 0.000 ARG M 190 *********************** 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 393 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 368 time to evaluate : 5.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 LYS cc_start: 0.7953 (tppp) cc_final: 0.7559 (mmtt) REVERT: F 485 GLN cc_start: 0.8726 (mt0) cc_final: 0.8453 (mt0) REVERT: M 258 ARG cc_start: 0.6813 (tpp80) cc_final: 0.6410 (tpp80) REVERT: O 283 ARG cc_start: 0.7404 (tpt90) cc_final: 0.6967 (tpt170) REVERT: R 485 GLN cc_start: 0.8638 (mt0) cc_final: 0.8303 (mt0) REVERT: S 449 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7979 (ttm170) REVERT: T 475 MET cc_start: 0.7666 (mmm) cc_final: 0.6959 (mmm) outliers start: 25 outliers final: 22 residues processed: 383 average time/residue: 0.8016 time to fit residues: 449.3008 Evaluate side-chains 378 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 356 time to evaluate : 5.268 ------------------------------------------------------------------------------- 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 H residue 518 LEU 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 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 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 W residue 451 ILE Chi-restraints excluded: chain X residue 486 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 9.9990 chunk 543 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 354 optimal weight: 0.6980 chunk 148 optimal weight: 0.0980 chunk 603 optimal weight: 0.7980 chunk 501 optimal weight: 0.9980 chunk 279 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 316 optimal weight: 50.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 43692 Z= 0.150 Angle : 0.353 8.387 58176 Z= 0.190 Chirality : 0.032 0.132 7980 Planarity : 0.002 0.050 6396 Dihedral : 2.401 14.168 6804 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.62 % Allowed : 5.75 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.78 (0.09), residues: 6252 helix: 4.53 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.44 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.004 0.001 PHE S 435 TYR 0.023 0.002 TYR T 517 ARG 0.016 0.000 ARG U 190 *********************** 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 413 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 387 time to evaluate : 5.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 LYS cc_start: 0.7946 (tppp) cc_final: 0.7589 (mmtt) REVERT: C 340 ARG cc_start: 0.7937 (mtm110) cc_final: 0.7734 (mtm110) REVERT: F 485 GLN cc_start: 0.8609 (mt0) cc_final: 0.8305 (mt0) REVERT: L 475 MET cc_start: 0.7702 (mmt) cc_final: 0.7498 (mmm) REVERT: M 336 ASN cc_start: 0.8537 (t0) cc_final: 0.8149 (t0) REVERT: O 287 GLU cc_start: 0.7222 (tp30) cc_final: 0.7017 (tp30) REVERT: Q 308 MET cc_start: 0.8269 (mtp) cc_final: 0.7899 (mtp) REVERT: R 485 GLN cc_start: 0.8540 (mt0) cc_final: 0.8267 (mt0) REVERT: T 475 MET cc_start: 0.7647 (mmm) cc_final: 0.7128 (mmm) REVERT: T 485 GLN cc_start: 0.8743 (mt0) cc_final: 0.8434 (mt0) outliers start: 26 outliers final: 17 residues processed: 402 average time/residue: 0.7398 time to fit residues: 450.2925 Evaluate side-chains 375 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 358 time to evaluate : 4.904 ------------------------------------------------------------------------------- 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 486 MET Chi-restraints excluded: chain H residue 518 LEU Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain J residue 486 MET Chi-restraints excluded: chain L residue 486 MET 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 R residue 486 MET Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 90.0000 chunk 68 optimal weight: 10.0000 chunk 343 optimal weight: 0.8980 chunk 440 optimal weight: 1.9990 chunk 341 optimal weight: 0.8980 chunk 508 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 chunk 601 optimal weight: 0.9980 chunk 376 optimal weight: 9.9990 chunk 366 optimal weight: 50.0000 chunk 277 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 43692 Z= 0.205 Angle : 0.389 10.626 58176 Z= 0.207 Chirality : 0.032 0.151 7980 Planarity : 0.002 0.049 6396 Dihedral : 2.432 17.477 6804 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.60 % Allowed : 6.49 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.68 (0.09), residues: 6252 helix: 4.47 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.35 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.008 0.001 PHE Q 435 TYR 0.021 0.002 TYR T 517 ARG 0.013 0.000 ARG A 190 *********************** 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 397 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 372 time to evaluate : 5.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 LYS cc_start: 0.7919 (tppp) cc_final: 0.7608 (mmtt) REVERT: F 485 GLN cc_start: 0.8662 (mt0) cc_final: 0.8365 (mt0) REVERT: H 479 LEU cc_start: 0.8497 (tt) cc_final: 0.8259 (tp) REVERT: M 190 ARG cc_start: 0.7267 (mtm110) cc_final: 0.7063 (mtm110) REVERT: M 258 ARG cc_start: 0.6690 (tpp80) cc_final: 0.6354 (tpp80) REVERT: M 336 ASN cc_start: 0.8591 (t0) cc_final: 0.8259 (t0) REVERT: Q 308 MET cc_start: 0.8258 (mtp) cc_final: 0.7854 (mtp) REVERT: R 485 GLN cc_start: 0.8601 (mt0) cc_final: 0.8329 (mt0) REVERT: T 475 MET cc_start: 0.7637 (mmm) cc_final: 0.7212 (mmm) outliers start: 25 outliers final: 22 residues processed: 388 average time/residue: 0.7843 time to fit residues: 450.0552 Evaluate side-chains 362 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 340 time to evaluate : 5.015 ------------------------------------------------------------------------------- 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 D residue 491 ASP 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 486 MET Chi-restraints excluded: chain H residue 518 LEU 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 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 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 S residue 345 SER Chi-restraints excluded: chain V residue 510 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 chunk 359 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 382 optimal weight: 2.9990 chunk 409 optimal weight: 20.0000 chunk 297 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 472 optimal weight: 50.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 43692 Z= 0.249 Angle : 0.414 9.766 58176 Z= 0.218 Chirality : 0.033 0.190 7980 Planarity : 0.002 0.054 6396 Dihedral : 2.486 18.486 6804 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.74 % Allowed : 6.54 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.51 (0.09), residues: 6252 helix: 4.36 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.36 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 422 PHE 0.010 0.002 PHE Q 435 TYR 0.020 0.002 TYR B 517 ARG 0.012 0.000 ARG I 190 *********************** 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 385 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 354 time to evaluate : 4.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 LYS cc_start: 0.7986 (tppp) cc_final: 0.7538 (mmtt) REVERT: C 340 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7703 (mtm110) REVERT: F 485 GLN cc_start: 0.8697 (mt0) cc_final: 0.8391 (mt0) REVERT: M 258 ARG cc_start: 0.6775 (tpp80) cc_final: 0.6408 (tpp80) REVERT: Q 308 MET cc_start: 0.8276 (mtp) cc_final: 0.7854 (mtp) REVERT: R 485 GLN cc_start: 0.8650 (mt0) cc_final: 0.8292 (mt0) REVERT: T 485 GLN cc_start: 0.8724 (mt0) cc_final: 0.8454 (mt0) outliers start: 31 outliers final: 27 residues processed: 373 average time/residue: 0.8040 time to fit residues: 436.4249 Evaluate side-chains 366 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 339 time to evaluate : 5.065 ------------------------------------------------------------------------------- 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 510 GLU 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 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 486 MET 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 J residue 486 MET 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 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 S residue 345 SER Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 486 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 0.7980 chunk 576 optimal weight: 50.0000 chunk 525 optimal weight: 50.0000 chunk 560 optimal weight: 5.9990 chunk 337 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 440 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 506 optimal weight: 1.9990 chunk 530 optimal weight: 50.0000 chunk 558 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 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** R 525 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 43692 Z= 0.224 Angle : 0.408 9.625 58176 Z= 0.217 Chirality : 0.033 0.198 7980 Planarity : 0.003 0.055 6396 Dihedral : 2.469 17.252 6804 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.67 % Allowed : 6.80 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.54 (0.09), residues: 6252 helix: 4.38 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.40 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 422 PHE 0.009 0.001 PHE Q 435 TYR 0.020 0.002 TYR B 517 ARG 0.016 0.000 ARG O 190 *********************** 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 380 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 352 time to evaluate : 5.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 LYS cc_start: 0.8020 (tppp) cc_final: 0.7658 (mmtt) REVERT: C 340 ARG cc_start: 0.7937 (mtm110) cc_final: 0.7655 (mtm110) REVERT: F 485 GLN cc_start: 0.8686 (mt0) cc_final: 0.8377 (mt0) REVERT: I 183 ARG cc_start: 0.6515 (mmm-85) cc_final: 0.6277 (tpt170) REVERT: I 240 ARG cc_start: 0.6363 (ttp80) cc_final: 0.6159 (ttp80) REVERT: M 194 GLU cc_start: 0.5924 (mm-30) cc_final: 0.5708 (mm-30) REVERT: M 258 ARG cc_start: 0.6727 (tpp80) cc_final: 0.6376 (tpp80) REVERT: Q 308 MET cc_start: 0.8292 (mtp) cc_final: 0.7899 (mtp) REVERT: R 485 GLN cc_start: 0.8640 (mt0) cc_final: 0.8386 (mt0) REVERT: T 485 GLN cc_start: 0.8748 (mt0) cc_final: 0.8434 (mt0) REVERT: U 190 ARG cc_start: 0.6910 (mtm110) cc_final: 0.6623 (mtm-85) outliers start: 28 outliers final: 24 residues processed: 370 average time/residue: 0.8030 time to fit residues: 436.2073 Evaluate side-chains 368 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 344 time to evaluate : 5.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 510 GLU 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 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 486 MET 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 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 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 S residue 345 SER Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 486 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 50.0000 chunk 592 optimal weight: 0.9980 chunk 361 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 chunk 411 optimal weight: 2.9990 chunk 621 optimal weight: 2.9990 chunk 572 optimal weight: 110.0000 chunk 495 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 382 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 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 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 525 GLN ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 525 GLN ** M 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 43692 Z= 0.205 Angle : 0.403 9.550 58176 Z= 0.215 Chirality : 0.033 0.196 7980 Planarity : 0.003 0.067 6396 Dihedral : 2.456 16.849 6804 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.72 % Allowed : 7.04 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.60 (0.09), residues: 6252 helix: 4.42 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.43 (0.22), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 422 PHE 0.008 0.001 PHE Q 435 TYR 0.019 0.002 TYR B 517 ARG 0.014 0.000 ARG I 190 ********************** 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 384 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 354 time to evaluate : 5.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 LYS cc_start: 0.8037 (tppp) cc_final: 0.7617 (mmtt) REVERT: C 340 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7704 (mtm110) REVERT: F 485 GLN cc_start: 0.8674 (mt0) cc_final: 0.8359 (mt0) REVERT: K 194 GLU cc_start: 0.5830 (mm-30) cc_final: 0.5608 (mm-30) REVERT: M 336 ASN cc_start: 0.8576 (t0) cc_final: 0.8237 (t0) REVERT: Q 308 MET cc_start: 0.8282 (mtp) cc_final: 0.7889 (mtp) REVERT: R 485 GLN cc_start: 0.8622 (mt0) cc_final: 0.8363 (mt0) outliers start: 30 outliers final: 27 residues processed: 374 average time/residue: 0.8058 time to fit residues: 446.3064 Evaluate side-chains 369 residues out of total 5424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 342 time to evaluate : 5.126 ------------------------------------------------------------------------------- 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 510 GLU 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 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 486 MET 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 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 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 S residue 345 SER Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 486 MET 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 393 optimal weight: 2.9990 chunk 527 optimal weight: 40.0000 chunk 151 optimal weight: 2.9990 chunk 456 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 495 optimal weight: 0.7980 chunk 207 optimal weight: 9.9990 chunk 509 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 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 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 = 0.4622 r_free = 0.4622 target = 0.248621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.197131 restraints weight = 43912.386| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.87 r_work: 0.3830 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 43692 Z= 0.205 Angle : 0.399 8.875 58176 Z= 0.214 Chirality : 0.033 0.215 7980 Planarity : 0.003 0.066 6396 Dihedral : 2.461 19.786 6804 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.65 % Allowed : 7.11 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.63 (0.09), residues: 6252 helix: 4.44 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.40 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 422 PHE 0.008 0.001 PHE Q 435 TYR 0.019 0.002 TYR B 517 ARG 0.014 0.000 ARG I 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9022.64 seconds wall clock time: 166 minutes 5.14 seconds (9965.14 seconds total)