Starting phenix.real_space_refine on Sun Mar 24 18:40:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwy_27031/03_2024/8cwy_27031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwy_27031/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwy_27031/03_2024/8cwy_27031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwy_27031/03_2024/8cwy_27031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwy_27031/03_2024/8cwy_27031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cwy_27031/03_2024/8cwy_27031.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 21.67, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 18.84 Conformation dependent library (CDL) restraints added in 8.6 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: 3.35 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: 15.02 Time building geometry restraints manager: 20.03 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: 99.97 - 106.24: 156 106.24 - 112.52: 26032 112.52 - 118.79: 12454 118.79 - 125.06: 19475 125.06 - 131.33: 59 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 2.440 nonbonded pdb=" OG SER Q 248 " pdb=" OE2 GLU R 506 " model vdw 2.028 2.440 nonbonded pdb=" OG SER W 186 " pdb=" NH1 ARG W 190 " model vdw 2.185 2.520 nonbonded pdb=" OG SER U 186 " pdb=" NH1 ARG U 190 " model vdw 2.187 2.520 nonbonded pdb=" OG SER K 186 " pdb=" NH1 ARG K 190 " model vdw 2.192 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.620 Check model and map are aligned: 0.610 Set scattering table: 0.410 Process input model: 109.320 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.400 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.370 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 503 time to evaluate : 4.590 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: 0.8665 time to fit residues: 625.0943 Evaluate side-chains 378 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 5.324 ------------------------------------------------------------------------------- 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: 0.9980 chunk 489 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 297 optimal weight: 0.9990 chunk 364 optimal weight: 100.0000 chunk 566 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 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 336 ASN ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** 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: 0.6035 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 43692 Z= 0.322 Angle : 0.467 6.143 58176 Z= 0.241 Chirality : 0.034 0.123 7980 Planarity : 0.003 0.024 6396 Dihedral : 2.645 35.585 6806 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.57 % Allowed : 3.11 % 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: 5.95 (0.09), residues: 6252 helix: 3.98 (0.06), residues: 5916 sheet: None (None), residues: 0 loop : 0.92 (0.21), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.008 0.002 PHE Q 435 TYR 0.021 0.002 TYR P 517 ARG 0.008 0.000 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 423 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 399 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7408 (tpt90) cc_final: 0.6818 (tpt170) REVERT: C 243 LYS cc_start: 0.7863 (tppp) cc_final: 0.7522 (mmtt) REVERT: C 340 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7648 (mtm110) REVERT: F 485 GLN cc_start: 0.8767 (mt0) cc_final: 0.8479 (mt0) REVERT: I 283 ARG cc_start: 0.7358 (tpt90) cc_final: 0.6786 (tpt170) REVERT: I 287 GLU cc_start: 0.7095 (tp30) cc_final: 0.6852 (tp30) REVERT: I 378 MET cc_start: 0.6621 (tpt) cc_final: 0.6163 (tpt) REVERT: K 233 ARG cc_start: 0.7288 (tpt170) cc_final: 0.6396 (tpt170) REVERT: K 283 ARG cc_start: 0.7484 (tpt90) cc_final: 0.7003 (tpt170) REVERT: M 283 ARG cc_start: 0.7375 (tpt90) cc_final: 0.6776 (tpt170) REVERT: R 485 GLN cc_start: 0.8695 (mt0) cc_final: 0.8451 (mt0) REVERT: S 283 ARG cc_start: 0.7430 (tpt90) cc_final: 0.7020 (tpt170) REVERT: T 475 MET cc_start: 0.7667 (mmm) cc_final: 0.7237 (mmm) REVERT: U 287 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6940 (mm-30) outliers start: 24 outliers final: 16 residues processed: 415 average time/residue: 0.7581 time to fit residues: 462.3115 Evaluate side-chains 364 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 348 time to evaluate : 4.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain I residue 347 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 T residue 486 MET Chi-restraints excluded: chain U residue 347 SER Chi-restraints excluded: chain W residue 347 SER 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: 5.9990 chunk 471 optimal weight: 0.0010 chunk 385 optimal weight: 8.9990 chunk 156 optimal weight: 90.0000 chunk 567 optimal weight: 0.7980 chunk 613 optimal weight: 8.9990 chunk 505 optimal weight: 1.9990 chunk 562 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 455 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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** T 525 GLN ** 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** W 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 43692 Z= 0.165 Angle : 0.368 9.580 58176 Z= 0.198 Chirality : 0.032 0.106 7980 Planarity : 0.002 0.031 6396 Dihedral : 2.475 26.812 6806 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.67 % Allowed : 3.64 % Favored : 95.69 % 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: 6.55 (0.09), residues: 6252 helix: 4.37 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.89 (0.22), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.003 0.001 PHE Q 435 TYR 0.021 0.002 TYR V 517 ARG 0.005 0.000 ARG M 190 *********************** 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 410 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 382 time to evaluate : 4.658 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: C 243 LYS cc_start: 0.7957 (tppp) cc_final: 0.7539 (mmtt) REVERT: F 485 GLN cc_start: 0.8631 (mt0) cc_final: 0.8330 (mt0) REVERT: I 378 MET cc_start: 0.6354 (tpt) cc_final: 0.5912 (tpt) REVERT: M 336 ASN cc_start: 0.8631 (t0) cc_final: 0.8213 (t0) REVERT: O 340 ARG cc_start: 0.7797 (mtm110) cc_final: 0.7596 (mtm110) REVERT: R 485 GLN cc_start: 0.8532 (mt0) cc_final: 0.8319 (mt0) REVERT: T 480 LYS cc_start: 0.8198 (mttp) cc_final: 0.7910 (mttt) REVERT: T 485 GLN cc_start: 0.8606 (mt0) cc_final: 0.8343 (mt0) REVERT: U 336 ASN cc_start: 0.8233 (t0) cc_final: 0.7624 (t0) outliers start: 28 outliers final: 12 residues processed: 400 average time/residue: 0.7062 time to fit residues: 424.5186 Evaluate side-chains 359 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 347 time to evaluate : 4.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 491 ASP Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain 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: 4.9990 chunk 426 optimal weight: 80.0000 chunk 294 optimal weight: 6.9990 chunk 62 optimal weight: 50.0000 chunk 270 optimal weight: 90.0000 chunk 381 optimal weight: 4.9990 chunk 569 optimal weight: 3.9990 chunk 603 optimal weight: 0.9980 chunk 297 optimal weight: 0.8980 chunk 539 optimal weight: 3.9990 chunk 162 optimal weight: 0.0370 overall best weight: 1.9862 ------------------------------------------------------------------------------- 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** H 525 GLN ** 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 43692 Z= 0.288 Angle : 0.430 9.863 58176 Z= 0.222 Chirality : 0.034 0.145 7980 Planarity : 0.002 0.028 6396 Dihedral : 2.544 18.680 6804 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.69 % Allowed : 4.48 % Favored : 94.83 % 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: 6.27 (0.09), residues: 6252 helix: 4.19 (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 0.010 0.002 PHE S 435 TYR 0.021 0.002 TYR T 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 384 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 355 time to evaluate : 5.103 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: C 243 LYS cc_start: 0.7977 (tppp) cc_final: 0.7571 (mmtt) REVERT: F 485 GLN cc_start: 0.8726 (mt0) cc_final: 0.8439 (mt0) REVERT: O 340 ARG cc_start: 0.7793 (mtm110) cc_final: 0.7513 (mtm110) REVERT: R 485 GLN cc_start: 0.8656 (mt0) cc_final: 0.8338 (mt0) outliers start: 29 outliers final: 21 residues processed: 377 average time/residue: 0.7416 time to fit residues: 412.5238 Evaluate side-chains 351 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 330 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 482 LEU 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 345 SER Chi-restraints excluded: chain H residue 491 ASP Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain J residue 486 MET Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain X residue 486 MET Chi-restraints excluded: chain X residue 491 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 1.9990 chunk 342 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 449 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 514 optimal weight: 3.9990 chunk 416 optimal weight: 110.0000 chunk 0 optimal weight: 120.0000 chunk 307 optimal weight: 0.9990 chunk 541 optimal weight: 10.0000 chunk 152 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 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** ** R 525 GLN ** 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: 0.5978 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 43692 Z= 0.198 Angle : 0.372 8.402 58176 Z= 0.197 Chirality : 0.032 0.123 7980 Planarity : 0.002 0.034 6396 Dihedral : 2.455 15.842 6804 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.74 % Allowed : 5.17 % Favored : 94.09 % 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 : 0.54 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.007 0.001 PHE Q 435 TYR 0.021 0.002 TYR T 517 ARG 0.006 0.000 ARG M 340 *********************** 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 402 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 371 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 LYS cc_start: 0.7942 (tppp) cc_final: 0.7570 (mmtt) REVERT: F 485 GLN cc_start: 0.8673 (mt0) cc_final: 0.8388 (mt0) REVERT: M 336 ASN cc_start: 0.8568 (t0) cc_final: 0.8210 (t0) REVERT: O 340 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7545 (mtm110) REVERT: R 485 GLN cc_start: 0.8603 (mt0) cc_final: 0.8354 (mt0) REVERT: S 233 ARG cc_start: 0.7213 (tpt170) cc_final: 0.6981 (tpt170) REVERT: T 475 MET cc_start: 0.7647 (mmm) cc_final: 0.6909 (mmm) outliers start: 31 outliers final: 24 residues processed: 392 average time/residue: 0.7540 time to fit residues: 444.5607 Evaluate side-chains 386 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 362 time to evaluate : 4.990 ------------------------------------------------------------------------------- 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 482 LEU Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain H residue 491 ASP Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain 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 N residue 491 ASP Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain 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: 0.8980 chunk 119 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 603 optimal weight: 0.5980 chunk 501 optimal weight: 0.9980 chunk 279 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 316 optimal weight: 50.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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** 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** V 485 GLN ** 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: 0.5956 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43692 Z= 0.172 Angle : 0.355 9.540 58176 Z= 0.190 Chirality : 0.032 0.119 7980 Planarity : 0.002 0.031 6396 Dihedral : 2.401 15.624 6804 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.81 % Allowed : 5.17 % Favored : 94.01 % 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: 6.69 (0.09), residues: 6252 helix: 4.48 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.39 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 422 PHE 0.006 0.001 PHE Q 435 TYR 0.023 0.002 TYR T 517 ARG 0.007 0.000 ARG C 183 *********************** 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 401 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 367 time to evaluate : 4.818 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: 0.7954 (tppp) cc_final: 0.7559 (mmtt) REVERT: F 485 GLN cc_start: 0.8648 (mt0) cc_final: 0.8354 (mt0) REVERT: M 336 ASN cc_start: 0.8526 (t0) cc_final: 0.8131 (t0) REVERT: Q 293 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7503 (mmtp) REVERT: R 485 GLN cc_start: 0.8582 (mt0) cc_final: 0.8331 (mt0) REVERT: T 475 MET cc_start: 0.7628 (mmm) cc_final: 0.7082 (mmm) outliers start: 34 outliers final: 28 residues processed: 390 average time/residue: 0.7667 time to fit residues: 445.5645 Evaluate side-chains 376 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 348 time to evaluate : 4.895 ------------------------------------------------------------------------------- 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 482 LEU 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 F residue 491 ASP 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 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 P residue 491 ASP Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain X residue 486 MET Chi-restraints excluded: chain X residue 491 ASP 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: 6.9990 chunk 343 optimal weight: 0.6980 chunk 440 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 508 optimal weight: 2.9990 chunk 337 optimal weight: 0.7980 chunk 601 optimal weight: 0.9990 chunk 376 optimal weight: 8.9990 chunk 366 optimal weight: 50.0000 chunk 277 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 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: 0.5970 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43692 Z= 0.193 Angle : 0.367 9.889 58176 Z= 0.195 Chirality : 0.032 0.129 7980 Planarity : 0.002 0.041 6396 Dihedral : 2.407 16.497 6804 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.03 % Allowed : 5.34 % 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: 6.64 (0.09), residues: 6252 helix: 4.45 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.27 (0.21), 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 0.020 0.002 TYR T 517 ARG 0.008 0.000 ARG A 240 *********************** 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 418 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 375 time to evaluate : 5.006 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: 0.7894 (tppp) cc_final: 0.7579 (mmtt) REVERT: F 485 GLN cc_start: 0.8665 (mt0) cc_final: 0.8351 (mt0) REVERT: H 479 LEU cc_start: 0.8526 (tt) cc_final: 0.8297 (tp) REVERT: M 336 ASN cc_start: 0.8553 (t0) cc_final: 0.8198 (t0) REVERT: R 485 GLN cc_start: 0.8615 (mt0) cc_final: 0.8366 (mt0) REVERT: T 475 MET cc_start: 0.7596 (mmm) cc_final: 0.7175 (mmm) outliers start: 43 outliers final: 38 residues processed: 404 average time/residue: 0.7121 time to fit residues: 428.5503 Evaluate side-chains 393 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 355 time to evaluate : 5.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain F residue 491 ASP 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 I residue 345 SER Chi-restraints excluded: chain J residue 486 MET Chi-restraints excluded: chain K residue 347 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain L residue 486 MET Chi-restraints excluded: chain L residue 491 ASP Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 491 ASP Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain P residue 491 ASP Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain T residue 491 ASP Chi-restraints excluded: chain U residue 347 SER Chi-restraints excluded: chain V residue 510 GLU Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 486 MET Chi-restraints excluded: chain X residue 491 ASP 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: 1.9990 chunk 181 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 382 optimal weight: 1.9990 chunk 409 optimal weight: 10.0000 chunk 297 optimal weight: 0.9990 chunk 56 optimal weight: 50.0000 chunk 472 optimal weight: 50.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 HIS I 422 HIS ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 HIS M 422 HIS ** O 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 525 GLN ** Q 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 43692 Z= 0.400 Angle : 0.506 9.557 58176 Z= 0.259 Chirality : 0.036 0.221 7980 Planarity : 0.003 0.037 6396 Dihedral : 2.667 22.286 6804 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.13 % Allowed : 5.53 % Favored : 93.34 % 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: 5.87 (0.09), residues: 6252 helix: 3.98 (0.06), residues: 5892 sheet: None (None), residues: 0 loop : 0.13 (0.19), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 422 PHE 0.014 0.002 PHE U 435 TYR 0.021 0.002 TYR T 517 ARG 0.011 0.000 ARG M 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 398 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 351 time to evaluate : 4.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 243 LYS cc_start: 0.8038 (tppp) cc_final: 0.7689 (mmtt) REVERT: K 449 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.8095 (ttm170) REVERT: R 485 GLN cc_start: 0.8769 (mt0) cc_final: 0.8540 (mt0) REVERT: V 500 ARG cc_start: 0.8433 (mtp180) cc_final: 0.8228 (mtp180) outliers start: 47 outliers final: 41 residues processed: 387 average time/residue: 0.7600 time to fit residues: 430.5329 Evaluate side-chains 377 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 336 time to evaluate : 4.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain F residue 491 ASP Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain H residue 491 ASP Chi-restraints excluded: chain H residue 518 LEU Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain J residue 486 MET Chi-restraints excluded: chain K residue 347 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain L residue 491 ASP Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain N residue 491 ASP Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain P residue 491 ASP Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain T residue 491 ASP Chi-restraints excluded: chain U residue 347 SER Chi-restraints excluded: chain V residue 491 ASP Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 486 MET Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 504 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 6.9990 chunk 576 optimal weight: 0.9990 chunk 525 optimal weight: 50.0000 chunk 560 optimal weight: 4.9990 chunk 337 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 440 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 506 optimal weight: 0.5980 chunk 530 optimal weight: 80.0000 chunk 558 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** 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: 0.5974 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 43692 Z= 0.180 Angle : 0.379 9.500 58176 Z= 0.203 Chirality : 0.032 0.138 7980 Planarity : 0.003 0.061 6396 Dihedral : 2.456 15.048 6804 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.86 % Allowed : 5.99 % Favored : 93.15 % 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: 6.46 (0.09), residues: 6252 helix: 4.33 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.34 (0.22), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 422 PHE 0.007 0.001 PHE Q 435 TYR 0.023 0.002 TYR P 517 ARG 0.017 0.000 ARG M 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 391 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 355 time to evaluate : 5.061 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: 0.8034 (tppp) cc_final: 0.7730 (mmtt) REVERT: F 485 GLN cc_start: 0.8693 (mt0) cc_final: 0.8415 (mt0) REVERT: H 479 LEU cc_start: 0.8519 (tt) cc_final: 0.8305 (tp) REVERT: M 190 ARG cc_start: 0.7528 (mtm110) cc_final: 0.7264 (mtm110) REVERT: M 336 ASN cc_start: 0.8551 (t0) cc_final: 0.8180 (t0) REVERT: R 485 GLN cc_start: 0.8572 (mt0) cc_final: 0.8289 (mt0) outliers start: 36 outliers final: 33 residues processed: 382 average time/residue: 0.7340 time to fit residues: 417.9168 Evaluate side-chains 375 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 342 time to evaluate : 5.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain F residue 491 ASP 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 J residue 491 ASP Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain L residue 491 ASP Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 491 ASP Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain P residue 491 ASP Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain T residue 491 ASP Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 486 MET Chi-restraints excluded: chain X residue 491 ASP 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: 0.9990 chunk 361 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 411 optimal weight: 2.9990 chunk 621 optimal weight: 0.9990 chunk 572 optimal weight: 110.0000 chunk 495 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 382 optimal weight: 0.9980 chunk 303 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** B 525 GLN ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 525 GLN N 525 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 43692 Z= 0.184 Angle : 0.382 9.995 58176 Z= 0.204 Chirality : 0.032 0.160 7980 Planarity : 0.003 0.074 6396 Dihedral : 2.424 16.343 6804 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.89 % Allowed : 6.32 % Favored : 92.79 % 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: 6.58 (0.09), residues: 6252 helix: 4.41 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.32 (0.23), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 422 PHE 0.007 0.001 PHE Q 435 TYR 0.023 0.002 TYR P 517 ARG 0.017 0.000 ARG O 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 386 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 349 time to evaluate : 4.741 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: 0.8039 (tppp) cc_final: 0.7666 (mmtt) REVERT: F 485 GLN cc_start: 0.8658 (mt0) cc_final: 0.8360 (mt0) REVERT: H 479 LEU cc_start: 0.8498 (tt) cc_final: 0.8283 (tp) REVERT: M 190 ARG cc_start: 0.7410 (mtm110) cc_final: 0.7168 (mtm110) REVERT: M 336 ASN cc_start: 0.8539 (t0) cc_final: 0.8172 (t0) REVERT: Q 293 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7481 (mmtp) REVERT: R 485 GLN cc_start: 0.8604 (mt0) cc_final: 0.8367 (mt0) outliers start: 37 outliers final: 36 residues processed: 377 average time/residue: 0.7361 time to fit residues: 409.9794 Evaluate side-chains 376 residues out of total 5424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 340 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 486 MET Chi-restraints excluded: chain F residue 491 ASP 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 510 GLU Chi-restraints excluded: chain H residue 518 LEU Chi-restraints excluded: chain I residue 345 SER Chi-restraints excluded: chain J residue 491 ASP Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain L residue 491 ASP Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 491 ASP Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain P residue 486 MET Chi-restraints excluded: chain P residue 491 ASP Chi-restraints excluded: chain R residue 486 MET Chi-restraints excluded: chain R residue 491 ASP Chi-restraints excluded: chain R residue 497 LEU Chi-restraints excluded: chain S residue 345 SER Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain T residue 486 MET Chi-restraints excluded: chain T residue 491 ASP Chi-restraints excluded: chain V residue 491 ASP Chi-restraints excluded: chain W residue 451 ILE Chi-restraints excluded: chain X residue 486 MET Chi-restraints excluded: chain X residue 491 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 0.9990 chunk 527 optimal weight: 50.0000 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: 0.6980 chunk 207 optimal weight: 5.9990 chunk 509 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** E 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.248155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.197662 restraints weight = 43862.136| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.94 r_work: 0.3825 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 43692 Z= 0.195 Angle : 0.392 10.231 58176 Z= 0.208 Chirality : 0.032 0.154 7980 Planarity : 0.003 0.097 6396 Dihedral : 2.428 15.516 6804 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.96 % Allowed : 6.25 % Favored : 92.79 % 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: 6.58 (0.09), residues: 6252 helix: 4.41 (0.05), residues: 5940 sheet: None (None), residues: 0 loop : 0.31 (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 0.023 0.002 TYR P 517 ARG 0.015 0.000 ARG O 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9219.06 seconds wall clock time: 166 minutes 36.57 seconds (9996.57 seconds total)