Starting phenix.real_space_refine (version: dev) on Wed Feb 22 11:51:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/02_2023/7n06_24101.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/02_2023/7n06_24101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/02_2023/7n06_24101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/02_2023/7n06_24101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/02_2023/7n06_24101.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/02_2023/7n06_24101.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.036 sd= 0.173 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 Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17223 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2744 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain: "B" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2744 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain: "C" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2744 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain: "D" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2744 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain: "E" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2744 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain: "F" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2744 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Classifications: {'DNA': 1, 'RNA': 2} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 2} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Classifications: {'DNA': 1, 'RNA': 2} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 2} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Classifications: {'DNA': 1, 'RNA': 2} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 2} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Classifications: {'DNA': 2, 'RNA': 1} Modifications used: {'5*END': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' A:plan2': 1, ' A:plan': 1, ' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Classifications: {'DNA': 2, 'RNA': 1} Modifications used: {'5*END': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' A:plan2': 1, ' A:plan': 1, ' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Classifications: {'DNA': 2, 'RNA': 1} Modifications used: {'5*END': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' A:plan2': 1, ' A:plan': 1, ' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 10.43, per 1000 atoms: 0.61 Number of scatterers: 17223 At special positions: 0 Unit cell: (110.329, 113.211, 124.738, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 12 15.00 O 3780 8.00 N 2697 7.00 C 10668 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: 7.46 Conformation dependent library (CDL) restraints added in 3.1 seconds 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 48 sheets defined 26.1% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.625A pdb=" N GLU A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.625A pdb=" N GLU B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.625A pdb=" N GLU C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 218 through 226 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 69 through 76 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 69 through 76 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 130 through 138 Processing helix chain 'F' and resid 208 through 217 Processing helix chain 'F' and resid 218 through 226 Processing helix chain 'F' and resid 232 through 237 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 299 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.667A pdb=" N VAL A 32 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.065A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP A 125 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.065A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP A 125 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 removed outlier: 7.871A pdb=" N THR A 99 " --> pdb=" O ILE A 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 267 removed outlier: 4.895A pdb=" N ILE A 281 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N CYS A 291 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP A 283 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER A 289 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 323 removed outlier: 7.266A pdb=" N SER A 329 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET A 331 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE A 342 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP A 333 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.667A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.065A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.065A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 100 removed outlier: 7.871A pdb=" N THR B 99 " --> pdb=" O ILE B 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 267 removed outlier: 4.895A pdb=" N ILE B 281 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N CYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 316 through 323 removed outlier: 7.266A pdb=" N SER B 329 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET B 331 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE B 342 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP B 333 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.667A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.065A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.065A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC3, first strand: chain 'C' and resid 99 through 100 removed outlier: 7.872A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 267 removed outlier: 4.895A pdb=" N ILE C 281 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N CYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 316 through 323 removed outlier: 7.267A pdb=" N SER C 329 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET C 331 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE C 342 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP C 333 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.671A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.176A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.176A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'D' and resid 99 through 100 removed outlier: 7.995A pdb=" N THR D 99 " --> pdb=" O ILE D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 267 removed outlier: 4.821A pdb=" N ILE D 281 " --> pdb=" O CYS D 291 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N CYS D 291 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP D 283 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER D 289 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 316 through 323 removed outlier: 7.148A pdb=" N SER D 329 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET D 331 " --> pdb=" O PHE D 342 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE D 342 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP D 333 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.672A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.176A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.176A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'E' and resid 99 through 100 removed outlier: 7.994A pdb=" N THR E 99 " --> pdb=" O ILE E 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 161 through 163 Processing sheet with id=AE3, first strand: chain 'E' and resid 264 through 267 removed outlier: 4.820A pdb=" N ILE E 281 " --> pdb=" O CYS E 291 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N CYS E 291 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP E 283 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER E 289 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 316 through 323 removed outlier: 7.148A pdb=" N SER E 329 " --> pdb=" O PRO E 344 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET E 331 " --> pdb=" O PHE E 342 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE E 342 " --> pdb=" O MET E 331 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP E 333 " --> pdb=" O GLU E 340 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.671A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.175A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.175A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'F' and resid 99 through 100 removed outlier: 7.994A pdb=" N THR F 99 " --> pdb=" O ILE F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 161 through 163 Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 267 removed outlier: 4.821A pdb=" N ILE F 281 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N CYS F 291 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP F 283 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER F 289 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 316 through 323 removed outlier: 7.149A pdb=" N SER F 329 " --> pdb=" O PRO F 344 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET F 331 " --> pdb=" O PHE F 342 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE F 342 " --> pdb=" O MET F 331 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TRP F 333 " --> pdb=" O GLU F 340 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1683 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: 6.12 Time building geometry restraints manager: 7.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5039 1.33 - 1.45: 2640 1.45 - 1.57: 9220 1.57 - 1.69: 24 1.69 - 1.81: 102 Bond restraints: 17025 Sorted by residual: bond pdb=" CB LYS B 47 " pdb=" CG LYS B 47 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" CB LYS C 47 " pdb=" CG LYS C 47 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" CB LYS A 47 " pdb=" CG LYS A 47 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.42e+00 bond pdb=" CG1 ILE C 27 " pdb=" CD1 ILE C 27 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.60e+00 bond pdb=" CG1 ILE B 27 " pdb=" CD1 ILE B 27 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00 ... (remaining 17020 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.86: 496 106.86 - 113.67: 9623 113.67 - 120.47: 6150 120.47 - 127.28: 6700 127.28 - 134.08: 161 Bond angle restraints: 23130 Sorted by residual: angle pdb=" C LEU E 201 " pdb=" N GLN E 202 " pdb=" CA GLN E 202 " ideal model delta sigma weight residual 120.38 123.89 -3.51 1.37e+00 5.33e-01 6.57e+00 angle pdb=" C LEU D 201 " pdb=" N GLN D 202 " pdb=" CA GLN D 202 " ideal model delta sigma weight residual 120.38 123.83 -3.45 1.37e+00 5.33e-01 6.36e+00 angle pdb=" C LEU F 201 " pdb=" N GLN F 202 " pdb=" CA GLN F 202 " ideal model delta sigma weight residual 120.38 123.83 -3.45 1.37e+00 5.33e-01 6.33e+00 angle pdb=" C THR F 49 " pdb=" N LEU F 50 " pdb=" CA LEU F 50 " ideal model delta sigma weight residual 121.48 125.90 -4.42 2.04e+00 2.40e-01 4.70e+00 angle pdb=" C THR E 49 " pdb=" N LEU E 50 " pdb=" CA LEU E 50 " ideal model delta sigma weight residual 121.48 125.89 -4.41 2.04e+00 2.40e-01 4.68e+00 ... (remaining 23125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 9354 17.89 - 35.78: 585 35.78 - 53.67: 132 53.67 - 71.56: 45 71.56 - 89.45: 42 Dihedral angle restraints: 10158 sinusoidal: 4116 harmonic: 6042 Sorted by residual: dihedral pdb=" CA PHE A 177 " pdb=" C PHE A 177 " pdb=" N ASN A 178 " pdb=" CA ASN A 178 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE B 177 " pdb=" C PHE B 177 " pdb=" N ASN B 178 " pdb=" CA ASN B 178 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE C 177 " pdb=" C PHE C 177 " pdb=" N ASN C 178 " pdb=" CA ASN C 178 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 10155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1266 0.033 - 0.067: 881 0.067 - 0.100: 358 0.100 - 0.134: 153 0.134 - 0.167: 6 Chirality restraints: 2664 Sorted by residual: chirality pdb=" CB ILE A 144 " pdb=" CA ILE A 144 " pdb=" CG1 ILE A 144 " pdb=" CG2 ILE A 144 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CB ILE C 144 " pdb=" CA ILE C 144 " pdb=" CG1 ILE C 144 " pdb=" CG2 ILE C 144 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CB ILE B 144 " pdb=" CA ILE B 144 " pdb=" CG1 ILE B 144 " pdb=" CG2 ILE B 144 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 2661 not shown) Planarity restraints: 2937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 118 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO C 119 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 118 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 119 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 118 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO B 119 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.021 5.00e-02 4.00e+02 ... (remaining 2934 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 406 2.66 - 3.22: 16018 3.22 - 3.78: 29120 3.78 - 4.34: 42668 4.34 - 4.90: 63951 Nonbonded interactions: 152163 Sorted by model distance: nonbonded pdb=" OE1 GLU B 4 " pdb=" O HOH B 401 " model vdw 2.096 2.440 nonbonded pdb=" OE1 GLU C 4 " pdb=" O HOH C 401 " model vdw 2.097 2.440 nonbonded pdb=" OE1 GLU A 4 " pdb=" O HOH A 401 " model vdw 2.099 2.440 nonbonded pdb=" OD1 ASP F 92 " pdb=" O HOH F 401 " model vdw 2.106 2.440 nonbonded pdb=" OD1 ASP D 92 " pdb=" O HOH D 401 " model vdw 2.106 2.440 ... (remaining 152158 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 401 through 402) selection = (chain 'H' and resid 401 through 402) selection = (chain 'I' and resid 401 through 402) selection = (chain 'J' and resid 401 through 402) selection = (chain 'K' and resid 401 through 402) selection = (chain 'L' and resid 401 through 402) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 66 5.16 5 C 10668 2.51 5 N 2697 2.21 5 O 3780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.420 Check model and map are aligned: 0.260 Process input model: 48.430 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 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 : 0.007 0.051 17025 Z= 0.483 Angle : 0.629 5.826 23130 Z= 0.345 Chirality : 0.051 0.167 2664 Planarity : 0.004 0.038 2937 Dihedral : 14.548 89.453 6258 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.39 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.80 (0.16), residues: 2070 helix: -1.82 (0.18), residues: 522 sheet: -0.23 (0.28), residues: 300 loop : -1.14 (0.15), residues: 1248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 240 time to evaluate : 2.076 Fit side-chains outliers start: 39 outliers final: 16 residues processed: 258 average time/residue: 1.5372 time to fit residues: 436.2573 Evaluate side-chains 200 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 6 residues processed: 10 average time/residue: 0.6642 time to fit residues: 10.7887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 159 optimal weight: 40.0000 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 119 optimal weight: 30.0000 chunk 185 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 338 HIS C 338 HIS D 20 GLN E 20 GLN F 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 17025 Z= 0.205 Angle : 0.522 4.334 23130 Z= 0.289 Chirality : 0.046 0.134 2664 Planarity : 0.003 0.026 2937 Dihedral : 6.177 47.489 2298 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.17), residues: 2070 helix: 0.00 (0.22), residues: 540 sheet: 0.48 (0.28), residues: 324 loop : -0.54 (0.16), residues: 1206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 2.121 Fit side-chains outliers start: 42 outliers final: 13 residues processed: 213 average time/residue: 1.4997 time to fit residues: 353.4164 Evaluate side-chains 193 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 2.112 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.1522 time to fit residues: 4.0374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 40.0000 chunk 154 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 165 optimal weight: 40.0000 chunk 184 optimal weight: 30.0000 chunk 63 optimal weight: 40.0000 chunk 148 optimal weight: 20.0000 overall best weight: 11.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS C 338 HIS ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 17025 Z= 0.364 Angle : 0.609 5.122 23130 Z= 0.338 Chirality : 0.051 0.183 2664 Planarity : 0.004 0.032 2937 Dihedral : 6.361 47.991 2298 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 2.54 % 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: -0.19 (0.18), residues: 2070 helix: 0.29 (0.23), residues: 540 sheet: 0.63 (0.30), residues: 294 loop : -0.46 (0.16), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 2.277 Fit side-chains outliers start: 47 outliers final: 14 residues processed: 212 average time/residue: 1.4758 time to fit residues: 345.8939 Evaluate side-chains 198 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 2.202 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.2103 time to fit residues: 4.6182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 20.0000 chunk 139 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 0.0470 chunk 124 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 overall best weight: 4.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 HIS D 137 ASN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 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 : 0.002 0.029 17025 Z= 0.160 Angle : 0.482 3.963 23130 Z= 0.268 Chirality : 0.045 0.136 2664 Planarity : 0.003 0.038 2937 Dihedral : 5.833 47.495 2298 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 2.00 % 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: 0.20 (0.18), residues: 2070 helix: 0.75 (0.24), residues: 540 sheet: 0.79 (0.28), residues: 324 loop : -0.28 (0.17), residues: 1206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 2.110 Fit side-chains outliers start: 37 outliers final: 12 residues processed: 216 average time/residue: 1.4870 time to fit residues: 357.6691 Evaluate side-chains 189 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.3252 time to fit residues: 3.3438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 40.0000 chunk 111 optimal weight: 0.4980 chunk 2 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 49 optimal weight: 0.2980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 17025 Z= 0.111 Angle : 0.435 4.036 23130 Z= 0.241 Chirality : 0.044 0.134 2664 Planarity : 0.003 0.040 2937 Dihedral : 5.366 47.526 2298 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 1.78 % 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: 0.47 (0.18), residues: 2070 helix: 1.01 (0.24), residues: 540 sheet: 1.11 (0.29), residues: 294 loop : -0.15 (0.17), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 2.007 Fit side-chains outliers start: 33 outliers final: 13 residues processed: 196 average time/residue: 1.3969 time to fit residues: 305.0514 Evaluate side-chains 177 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1542 time to fit residues: 3.1909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 197 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 338 HIS C 338 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17025 Z= 0.223 Angle : 0.514 3.957 23130 Z= 0.284 Chirality : 0.047 0.134 2664 Planarity : 0.003 0.042 2937 Dihedral : 5.778 47.653 2298 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 1.78 % 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: 0.37 (0.18), residues: 2070 helix: 0.89 (0.23), residues: 540 sheet: 0.91 (0.28), residues: 324 loop : -0.18 (0.17), residues: 1206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 2.044 Fit side-chains outliers start: 33 outliers final: 16 residues processed: 194 average time/residue: 1.4357 time to fit residues: 309.5310 Evaluate side-chains 181 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.1570 time to fit residues: 3.1655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 144 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 17025 Z= 0.152 Angle : 0.467 4.135 23130 Z= 0.258 Chirality : 0.045 0.134 2664 Planarity : 0.003 0.042 2937 Dihedral : 5.561 46.987 2298 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.40 % 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: 0.47 (0.18), residues: 2070 helix: 0.98 (0.24), residues: 540 sheet: 1.05 (0.29), residues: 294 loop : -0.12 (0.17), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 2.130 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 192 average time/residue: 1.3859 time to fit residues: 296.9219 Evaluate side-chains 180 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2261 time to fit residues: 3.2827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 125 optimal weight: 40.0000 chunk 133 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 HIS C 338 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 17025 Z= 0.252 Angle : 0.533 4.619 23130 Z= 0.295 Chirality : 0.048 0.141 2664 Planarity : 0.003 0.042 2937 Dihedral : 5.865 47.173 2298 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.62 % 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: 0.35 (0.18), residues: 2070 helix: 0.83 (0.23), residues: 540 sheet: 0.92 (0.28), residues: 324 loop : -0.18 (0.17), residues: 1206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 2.154 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 188 average time/residue: 1.4377 time to fit residues: 301.6624 Evaluate side-chains 182 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.2201 time to fit residues: 4.0032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 30.0000 chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 HIS C 338 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 17025 Z= 0.202 Angle : 0.506 4.853 23130 Z= 0.280 Chirality : 0.046 0.133 2664 Planarity : 0.003 0.042 2937 Dihedral : 5.768 47.055 2298 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.18), residues: 2070 helix: 0.85 (0.23), residues: 540 sheet: 1.07 (0.29), residues: 294 loop : -0.16 (0.17), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.953 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 183 average time/residue: 1.4253 time to fit residues: 289.9654 Evaluate side-chains 177 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 2.150 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.3042 time to fit residues: 3.3675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 40.0000 chunk 118 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 0.2980 chunk 203 optimal weight: 30.0000 chunk 187 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 16 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 6.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 HIS C 338 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 17025 Z= 0.230 Angle : 0.525 5.318 23130 Z= 0.290 Chirality : 0.047 0.147 2664 Planarity : 0.003 0.042 2937 Dihedral : 5.863 47.183 2298 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2070 helix: 0.80 (0.23), residues: 540 sheet: 1.07 (0.29), residues: 294 loop : -0.18 (0.17), residues: 1236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 2.119 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 177 average time/residue: 1.4143 time to fit residues: 279.8649 Evaluate side-chains 177 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 2.086 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.2573 time to fit residues: 3.6219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 162 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 20 optimal weight: 0.0020 chunk 29 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.128367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100717 restraints weight = 19590.690| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.28 r_work: 0.3092 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 17025 Z= 0.170 Angle : 0.484 5.149 23130 Z= 0.268 Chirality : 0.045 0.154 2664 Planarity : 0.003 0.042 2937 Dihedral : 5.660 47.058 2298 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2070 helix: 0.89 (0.24), residues: 540 sheet: 1.11 (0.29), residues: 294 loop : -0.12 (0.17), residues: 1236 =============================================================================== Job complete usr+sys time: 6258.93 seconds wall clock time: 112 minutes 3.39 seconds (6723.39 seconds total)