Starting phenix.real_space_refine on Tue Apr 9 19:40:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/04_2024/7n06_24101.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/04_2024/7n06_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_24101/04_2024/7n06_24101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/04_2024/7n06_24101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/04_2024/7n06_24101.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n06_24101/04_2024/7n06_24101.pdb" } resolution = 2.2 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 ------------------------------------------------------------------------------- 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 27 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: 27 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: 27 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: 51 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: 51 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: 51 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: 9.42, per 1000 atoms: 0.55 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: 7.23 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: 2.02 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: 5.88 Time building geometry restraints manager: 7.74 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: 9360 17.89 - 35.78: 586 35.78 - 53.67: 143 53.67 - 71.56: 51 71.56 - 89.45: 42 Dihedral angle restraints: 10182 sinusoidal: 4140 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 10179 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 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: 1.500 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: 0.010 Extract box with map and model: 6.840 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 47.840 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.110 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 : 14.751 89.453 6282 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 % Allowed : 7.44 % Favored : 90.45 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 87 HIS 0.007 0.002 HIS C 96 PHE 0.023 0.002 PHE B 16 TYR 0.012 0.002 TYR F 33 ARG 0.004 0.001 ARG C 62 *********************** 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 : 2.117 Fit side-chains REVERT: A 189 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: A 265 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: B 265 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: B 335 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7507 (ttpp) REVERT: C 265 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: D 225 ARG cc_start: 0.7159 (ttm170) cc_final: 0.6889 (ttm-80) REVERT: E 225 ARG cc_start: 0.7157 (ttm170) cc_final: 0.6934 (ttp-170) REVERT: F 225 ARG cc_start: 0.7161 (ttm170) cc_final: 0.6884 (ttm-80) outliers start: 39 outliers final: 16 residues processed: 258 average time/residue: 1.6224 time to fit residues: 459.7979 Evaluate side-chains 202 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain F residue 224 GLU 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: 0.8575 moved from start: 0.1248 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= 0.204 Angle : 0.520 4.372 23130 Z= 0.287 Chirality : 0.046 0.134 2664 Planarity : 0.003 0.026 2937 Dihedral : 8.569 63.485 2362 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.10 % Allowed : 11.60 % Favored : 86.30 % 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: -0.38 (0.17), residues: 2070 helix: -0.00 (0.22), residues: 540 sheet: 0.49 (0.28), residues: 324 loop : -0.53 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 333 HIS 0.019 0.002 HIS B 338 PHE 0.015 0.002 PHE C 16 TYR 0.012 0.001 TYR D 226 ARG 0.003 0.000 ARG D 258 *********************** 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 230 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 2.047 Fit side-chains REVERT: A 265 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7800 (pp20) REVERT: B 265 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7794 (pp20) REVERT: C 265 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7835 (pp20) REVERT: D 45 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: D 225 ARG cc_start: 0.7102 (ttm170) cc_final: 0.6812 (ttm-80) REVERT: E 45 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: F 45 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7162 (tm-30) outliers start: 39 outliers final: 14 residues processed: 212 average time/residue: 1.5387 time to fit residues: 358.9992 Evaluate side-chains 195 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 319 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 40.0000 chunk 154 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 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: 10.7192 ------------------------------------------------------------------------------- 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** ** 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: 0.8597 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17025 Z= 0.329 Angle : 0.589 5.428 23130 Z= 0.325 Chirality : 0.050 0.170 2664 Planarity : 0.004 0.033 2937 Dihedral : 8.294 68.217 2343 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.27 % Allowed : 12.35 % Favored : 85.38 % 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: -0.17 (0.18), residues: 2070 helix: 0.33 (0.23), residues: 540 sheet: 0.63 (0.30), residues: 294 loop : -0.46 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 87 HIS 0.008 0.002 HIS C 338 PHE 0.020 0.002 PHE C 16 TYR 0.014 0.002 TYR F 226 ARG 0.004 0.001 ARG B 139 *********************** 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 218 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.938 Fit side-chains REVERT: A 139 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7333 (ttm-80) REVERT: A 265 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: B 139 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7276 (ttm-80) REVERT: B 265 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: B 266 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8894 (tp) REVERT: C 265 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: D 45 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: D 146 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6874 (mm-30) REVERT: D 225 ARG cc_start: 0.7188 (ttm170) cc_final: 0.6956 (ttm-80) REVERT: E 45 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: E 146 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: F 45 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7266 (tm-30) outliers start: 42 outliers final: 13 residues processed: 204 average time/residue: 1.5318 time to fit residues: 345.0356 Evaluate side-chains 197 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 319 VAL 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: 0.6980 chunk 96 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS C 200 ASN C 338 HIS 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: 0.8571 moved from start: 0.1416 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= 0.201 Angle : 0.504 4.392 23130 Z= 0.279 Chirality : 0.046 0.134 2664 Planarity : 0.003 0.037 2937 Dihedral : 7.618 63.322 2340 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.27 % Allowed : 13.00 % Favored : 84.74 % 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: 0.15 (0.18), residues: 2070 helix: 0.69 (0.23), residues: 540 sheet: 0.77 (0.28), residues: 324 loop : -0.32 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 333 HIS 0.008 0.001 HIS C 338 PHE 0.015 0.002 PHE C 16 TYR 0.012 0.001 TYR F 226 ARG 0.002 0.000 ARG C 139 *********************** 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 220 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 2.050 Fit side-chains REVERT: B 139 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7264 (ttm-80) REVERT: D 45 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: D 225 ARG cc_start: 0.7122 (ttm170) cc_final: 0.6867 (ttm-80) REVERT: D 240 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7252 (t0) REVERT: E 45 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: F 45 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7146 (tm-30) outliers start: 42 outliers final: 14 residues processed: 207 average time/residue: 1.4463 time to fit residues: 332.7567 Evaluate side-chains 184 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 233 PHE Chi-restraints excluded: chain F residue 319 VAL 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: 5.9990 chunk 2 optimal weight: 7.9990 chunk 146 optimal weight: 0.0770 chunk 81 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- 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 E 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17025 Z= 0.130 Angle : 0.448 3.996 23130 Z= 0.248 Chirality : 0.044 0.135 2664 Planarity : 0.003 0.040 2937 Dihedral : 6.585 58.175 2331 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.46 % Allowed : 14.67 % Favored : 83.87 % 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: 0.41 (0.18), residues: 2070 helix: 0.93 (0.24), residues: 540 sheet: 1.08 (0.29), residues: 294 loop : -0.18 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 333 HIS 0.008 0.001 HIS C 338 PHE 0.010 0.001 PHE C 16 TYR 0.009 0.001 TYR F 226 ARG 0.001 0.000 ARG F 258 *********************** 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 198 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.968 Fit side-chains REVERT: D 45 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: E 45 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: F 45 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7121 (tm-30) outliers start: 27 outliers final: 6 residues processed: 192 average time/residue: 1.4634 time to fit residues: 311.8820 Evaluate side-chains 170 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 197 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17025 Z= 0.241 Angle : 0.526 4.719 23130 Z= 0.290 Chirality : 0.047 0.133 2664 Planarity : 0.003 0.042 2937 Dihedral : 6.977 58.596 2327 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.83 % Allowed : 15.53 % Favored : 82.63 % 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: 0.29 (0.18), residues: 2070 helix: 0.79 (0.23), residues: 540 sheet: 0.87 (0.28), residues: 324 loop : -0.22 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.007 0.001 HIS C 338 PHE 0.016 0.002 PHE C 16 TYR 0.015 0.002 TYR F 226 ARG 0.003 0.000 ARG B 139 *********************** 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 199 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.954 Fit side-chains REVERT: A 139 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7346 (ttm-80) REVERT: B 139 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7283 (ttm-80) REVERT: D 45 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: D 136 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7824 (ttp-170) REVERT: D 146 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: E 45 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: E 136 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7857 (ttp-170) REVERT: F 45 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: F 146 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6951 (mm-30) outliers start: 34 outliers final: 13 residues processed: 193 average time/residue: 1.4769 time to fit residues: 315.7501 Evaluate side-chains 184 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 144 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17025 Z= 0.186 Angle : 0.489 4.338 23130 Z= 0.270 Chirality : 0.046 0.133 2664 Planarity : 0.003 0.042 2937 Dihedral : 6.809 58.398 2327 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.62 % Allowed : 15.86 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2070 helix: 0.83 (0.23), residues: 540 sheet: 1.01 (0.29), residues: 294 loop : -0.17 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 333 HIS 0.007 0.001 HIS C 338 PHE 0.014 0.001 PHE C 16 TYR 0.012 0.001 TYR F 226 ARG 0.002 0.000 ARG C 139 *********************** 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 193 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.991 Fit side-chains REVERT: A 265 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7762 (pp20) REVERT: D 45 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: D 136 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7816 (ttp-170) REVERT: D 240 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7240 (t0) REVERT: E 45 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: E 136 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7849 (ttp-170) REVERT: F 45 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: F 146 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6953 (mm-30) outliers start: 30 outliers final: 15 residues processed: 188 average time/residue: 1.4050 time to fit residues: 294.0214 Evaluate side-chains 181 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 125 optimal weight: 40.0000 chunk 133 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17025 Z= 0.206 Angle : 0.503 4.644 23130 Z= 0.278 Chirality : 0.046 0.133 2664 Planarity : 0.003 0.042 2937 Dihedral : 6.880 58.473 2327 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.37 % Allowed : 15.16 % Favored : 82.47 % 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: 0.33 (0.18), residues: 2070 helix: 0.79 (0.23), residues: 540 sheet: 1.00 (0.29), residues: 294 loop : -0.18 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.007 0.001 HIS C 338 PHE 0.015 0.002 PHE C 16 TYR 0.012 0.001 TYR F 226 ARG 0.002 0.000 ARG B 139 *********************** 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 202 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 158 time to evaluate : 2.205 Fit side-chains REVERT: A 139 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7344 (ttm-80) REVERT: A 265 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7766 (pp20) REVERT: B 139 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7275 (ttm-80) REVERT: B 265 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7772 (pp20) REVERT: C 265 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7786 (pp20) REVERT: D 45 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: D 136 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7834 (ttp-170) REVERT: D 240 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7240 (t0) REVERT: E 45 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: E 136 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7850 (ttp-170) REVERT: F 45 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7250 (tm-30) outliers start: 44 outliers final: 15 residues processed: 195 average time/residue: 1.4664 time to fit residues: 316.5217 Evaluate side-chains 183 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 319 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 110 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 30.0000 chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: 0.8562 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17025 Z= 0.186 Angle : 0.490 5.225 23130 Z= 0.270 Chirality : 0.046 0.135 2664 Planarity : 0.003 0.042 2937 Dihedral : 6.797 58.398 2327 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 15.80 % Favored : 82.42 % 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: 0.83 (0.24), residues: 540 sheet: 1.03 (0.29), residues: 294 loop : -0.16 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 333 HIS 0.007 0.001 HIS C 338 PHE 0.014 0.001 PHE C 16 TYR 0.011 0.001 TYR F 226 ARG 0.002 0.000 ARG B 139 *********************** 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 192 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 2.124 Fit side-chains REVERT: A 139 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7342 (ttm-80) REVERT: A 265 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7762 (pp20) REVERT: B 265 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7763 (pp20) REVERT: C 265 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7788 (pp20) REVERT: D 45 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: D 136 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7783 (ttp-170) REVERT: D 240 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7238 (t0) REVERT: E 45 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: E 136 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7797 (ttp-170) REVERT: F 45 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7154 (tm-30) outliers start: 33 outliers final: 16 residues processed: 188 average time/residue: 1.4626 time to fit residues: 304.8904 Evaluate side-chains 183 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 40.0000 chunk 161 optimal weight: 50.0000 chunk 16 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17025 Z= 0.173 Angle : 0.481 5.734 23130 Z= 0.265 Chirality : 0.045 0.151 2664 Planarity : 0.003 0.042 2937 Dihedral : 6.726 58.345 2327 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 15.75 % Favored : 82.47 % 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: 0.40 (0.18), residues: 2070 helix: 0.87 (0.24), residues: 540 sheet: 1.05 (0.29), residues: 294 loop : -0.14 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 333 HIS 0.006 0.001 HIS C 338 PHE 0.013 0.001 PHE C 16 TYR 0.011 0.001 TYR E 226 ARG 0.002 0.000 ARG B 139 ********************** 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 189 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 2.077 Fit side-chains REVERT: A 139 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7345 (ttm-80) REVERT: A 265 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7759 (pp20) REVERT: B 265 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7758 (pp20) REVERT: C 265 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7788 (pp20) REVERT: D 45 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: D 136 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7790 (ttp-170) REVERT: D 146 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7000 (mm-30) REVERT: D 240 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7225 (t0) REVERT: E 45 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: E 136 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7805 (ttp-170) REVERT: F 45 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7152 (tm-30) outliers start: 33 outliers final: 18 residues processed: 181 average time/residue: 1.5010 time to fit residues: 301.5721 Evaluate side-chains 182 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 319 VAL 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: 3.9990 chunk 149 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.127919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100679 restraints weight = 19641.000| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.28 r_work: 0.3086 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17025 Z= 0.187 Angle : 0.492 5.404 23130 Z= 0.271 Chirality : 0.046 0.133 2664 Planarity : 0.003 0.042 2937 Dihedral : 6.779 58.400 2327 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.73 % Allowed : 15.91 % Favored : 82.36 % 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: 0.84 (0.24), residues: 540 sheet: 1.05 (0.29), residues: 294 loop : -0.15 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 333 HIS 0.008 0.001 HIS C 338 PHE 0.014 0.001 PHE C 16 TYR 0.012 0.001 TYR F 226 ARG 0.002 0.000 ARG F 139 =============================================================================== Job complete usr+sys time: 6457.28 seconds wall clock time: 117 minutes 18.15 seconds (7038.15 seconds total)