Starting phenix.real_space_refine on Wed Mar 4 23:04:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n06_24101/03_2026/7n06_24101.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n06_24101/03_2026/7n06_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 { model { file = "/net/cci-nas-00/data/ceres_data/7n06_24101/03_2026/7n06_24101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n06_24101/03_2026/7n06_24101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n06_24101/03_2026/7n06_24101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n06_24101/03_2026/7n06_24101.map" } 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 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. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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%5*END:plan': 1, ' A%5*END:plan2': 1, ' A:plan': 1, ' A:plan2': 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%5*END:plan': 1, ' A%5*END:plan2': 1, ' A:plan': 1, ' A:plan2': 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%5*END:plan': 1, ' A%5*END:plan2': 1, ' A:plan': 1, ' A:plan2': 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: 3.83, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 870.2 milliseconds 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: 0.54 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: 3.08 Time building geometry restraints manager: 2.00 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: 0.00 - 1.17: 21647 1.17 - 2.33: 1266 2.33 - 3.50: 168 3.50 - 4.66: 34 4.66 - 5.83: 15 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 3.040 nonbonded pdb=" OE1 GLU C 4 " pdb=" O HOH C 401 " model vdw 2.097 3.040 nonbonded pdb=" OE1 GLU A 4 " pdb=" O HOH A 401 " model vdw 2.099 3.040 nonbonded pdb=" OD1 ASP F 92 " pdb=" O HOH F 401 " model vdw 2.106 3.040 nonbonded pdb=" OD1 ASP D 92 " pdb=" O HOH D 401 " model vdw 2.106 3.040 ... (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 Time spend for trying shortcut: 0.03 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: 2.390 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: 0.880 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.660 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:7.840 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- 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= 0.323 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG C 62 TYR 0.012 0.002 TYR F 33 PHE 0.023 0.002 PHE B 16 TRP 0.009 0.002 TRP D 87 HIS 0.007 0.002 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00745 (17025) covalent geometry : angle 0.62942 (23130) hydrogen bonds : bond 0.20006 ( 594) hydrogen bonds : angle 8.02381 ( 1683) *********************** 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 to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 0.632 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: 0.7931 (tm-30) REVERT: D 225 ARG cc_start: 0.7159 (ttm170) cc_final: 0.6908 (ttm-80) REVERT: E 225 ARG cc_start: 0.7157 (ttm170) cc_final: 0.6951 (ttp-170) REVERT: F 225 ARG cc_start: 0.7161 (ttm170) cc_final: 0.6899 (ttm-80) outliers start: 39 outliers final: 13 residues processed: 258 average time/residue: 0.7392 time to fit residues: 208.3942 Evaluate side-chains 199 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 E residue 115 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 E 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095961 restraints weight = 19635.169| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.27 r_work: 0.3114 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1343 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= 0.154 Angle : 0.536 4.393 23130 Z= 0.298 Chirality : 0.047 0.135 2664 Planarity : 0.003 0.026 2937 Dihedral : 8.533 63.961 2353 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.73 % Allowed : 11.76 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.17), residues: 2070 helix: 0.11 (0.22), residues: 534 sheet: 0.47 (0.30), residues: 294 loop : -0.56 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 258 TYR 0.011 0.001 TYR F 226 PHE 0.018 0.002 PHE B 16 TRP 0.008 0.001 TRP B 333 HIS 0.021 0.002 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00337 (17025) covalent geometry : angle 0.53602 (23130) hydrogen bonds : bond 0.04974 ( 594) hydrogen bonds : angle 5.91457 ( 1683) *********************** 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 220 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.712 Fit side-chains REVERT: A 265 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: B 265 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: C 265 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8070 (pp20) REVERT: D 45 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: D 225 ARG cc_start: 0.6928 (ttm170) cc_final: 0.6618 (ttm-80) REVERT: E 45 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: F 45 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: F 225 ARG cc_start: 0.6882 (ttm170) cc_final: 0.6569 (ttm-80) outliers start: 32 outliers final: 11 residues processed: 204 average time/residue: 0.7231 time to fit residues: 161.7364 Evaluate side-chains 188 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 B residue 265 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 1 MET 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 1 MET 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 193 optimal weight: 50.0000 chunk 72 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 160 optimal weight: 50.0000 chunk 67 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 153 optimal weight: 0.0370 chunk 146 optimal weight: 9.9990 overall best weight: 3.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN C 200 ASN C 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101706 restraints weight = 19981.779| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.20 r_work: 0.3135 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1673 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= 0.107 Angle : 0.470 3.956 23130 Z= 0.260 Chirality : 0.045 0.134 2664 Planarity : 0.003 0.037 2937 Dihedral : 8.004 59.919 2335 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.73 % Allowed : 13.38 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2070 helix: 0.66 (0.23), residues: 540 sheet: 0.74 (0.28), residues: 324 loop : -0.32 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 258 TYR 0.011 0.001 TYR D 226 PHE 0.012 0.001 PHE B 16 TRP 0.007 0.001 TRP A 333 HIS 0.008 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00232 (17025) covalent geometry : angle 0.46960 (23130) hydrogen bonds : bond 0.04052 ( 594) hydrogen bonds : angle 5.32191 ( 1683) *********************** 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 216 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.720 Fit side-chains REVERT: C 317 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7616 (pttp) REVERT: D 4 GLU cc_start: 0.8458 (mp0) cc_final: 0.8092 (mp0) REVERT: D 45 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: D 225 ARG cc_start: 0.6939 (ttm170) cc_final: 0.6705 (ttm-80) REVERT: E 4 GLU cc_start: 0.8471 (mp0) cc_final: 0.8184 (mp0) REVERT: E 45 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: F 1 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7426 (mmm) REVERT: F 4 GLU cc_start: 0.8471 (mp0) cc_final: 0.8249 (mp0) REVERT: F 45 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: F 221 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7000 (mt-10) REVERT: F 225 ARG cc_start: 0.6903 (ttm170) cc_final: 0.6653 (ttm-80) outliers start: 32 outliers final: 10 residues processed: 204 average time/residue: 0.6532 time to fit residues: 147.3305 Evaluate side-chains 186 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 233 PHE 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 185 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 169 optimal weight: 0.0000 chunk 110 optimal weight: 20.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- 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 F 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100815 restraints weight = 19762.471| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.25 r_work: 0.3109 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1601 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= 0.146 Angle : 0.507 4.465 23130 Z= 0.280 Chirality : 0.047 0.134 2664 Planarity : 0.003 0.039 2937 Dihedral : 7.473 59.158 2325 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.78 % Allowed : 14.19 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2070 helix: 0.76 (0.24), residues: 540 sheet: 0.81 (0.30), residues: 294 loop : -0.28 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.013 0.001 TYR F 226 PHE 0.015 0.002 PHE A 16 TRP 0.006 0.001 TRP B 333 HIS 0.008 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00323 (17025) covalent geometry : angle 0.50675 (23130) hydrogen bonds : bond 0.04526 ( 594) hydrogen bonds : angle 5.39266 ( 1683) *********************** 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 211 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.795 Fit side-chains REVERT: B 139 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7934 (ttm-80) REVERT: D 4 GLU cc_start: 0.8476 (mp0) cc_final: 0.8170 (mp0) REVERT: D 45 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: D 225 ARG cc_start: 0.6973 (ttm170) cc_final: 0.6710 (ttm-80) REVERT: E 4 GLU cc_start: 0.8487 (mp0) cc_final: 0.8167 (mp0) REVERT: E 45 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: E 146 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7178 (mm-30) REVERT: E 221 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6988 (mt-10) REVERT: F 4 GLU cc_start: 0.8485 (mp0) cc_final: 0.8198 (mp0) REVERT: F 45 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: F 221 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6994 (mt-10) REVERT: F 225 ARG cc_start: 0.6945 (ttm170) cc_final: 0.6639 (ttm-80) outliers start: 33 outliers final: 12 residues processed: 202 average time/residue: 0.6743 time to fit residues: 150.1212 Evaluate side-chains 189 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 221 GLU 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 D residue 148 SER Chi-restraints excluded: chain D residue 198 SER 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 198 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 198 SER 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 74 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 34 optimal weight: 40.0000 chunk 165 optimal weight: 40.0000 chunk 105 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 D 137 ASN D 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.129734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.102783 restraints weight = 19779.870| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.25 r_work: 0.3146 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1879 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= 0.096 Angle : 0.449 4.020 23130 Z= 0.249 Chirality : 0.045 0.133 2664 Planarity : 0.003 0.040 2937 Dihedral : 6.934 59.879 2325 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.67 % Allowed : 14.62 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2070 helix: 0.93 (0.24), residues: 540 sheet: 1.07 (0.29), residues: 294 loop : -0.19 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 258 TYR 0.010 0.001 TYR F 226 PHE 0.010 0.001 PHE A 16 TRP 0.007 0.001 TRP B 333 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00206 (17025) covalent geometry : angle 0.44928 (23130) hydrogen bonds : bond 0.03600 ( 594) hydrogen bonds : angle 5.06674 ( 1683) *********************** 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 211 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.617 Fit side-chains REVERT: D 4 GLU cc_start: 0.8421 (mp0) cc_final: 0.8091 (mp0) REVERT: D 45 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: E 1 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7430 (mmm) REVERT: E 4 GLU cc_start: 0.8459 (mp0) cc_final: 0.8116 (mp0) REVERT: E 45 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: E 47 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8988 (mmmm) REVERT: F 1 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7422 (mmm) REVERT: F 4 GLU cc_start: 0.8453 (mp0) cc_final: 0.8145 (mp0) REVERT: F 45 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7948 (tm-30) outliers start: 31 outliers final: 12 residues processed: 200 average time/residue: 0.6659 time to fit residues: 146.9167 Evaluate side-chains 183 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 1 MET 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 319 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 185 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 161 optimal weight: 50.0000 chunk 115 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.127072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099916 restraints weight = 19651.915| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.27 r_work: 0.3086 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1615 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= 0.182 Angle : 0.535 4.272 23130 Z= 0.296 Chirality : 0.048 0.142 2664 Planarity : 0.003 0.041 2937 Dihedral : 7.280 58.602 2325 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.83 % Allowed : 14.78 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2070 helix: 0.78 (0.23), residues: 540 sheet: 0.85 (0.30), residues: 294 loop : -0.24 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.014 0.002 TYR D 226 PHE 0.018 0.002 PHE A 16 TRP 0.006 0.001 TRP E 87 HIS 0.008 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00409 (17025) covalent geometry : angle 0.53489 (23130) hydrogen bonds : bond 0.04791 ( 594) hydrogen bonds : angle 5.44331 ( 1683) *********************** 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 203 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.629 Fit side-chains REVERT: A 139 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7984 (ttm-80) REVERT: B 139 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7953 (ttm-80) REVERT: D 4 GLU cc_start: 0.8484 (mp0) cc_final: 0.8143 (mp0) REVERT: D 45 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: D 146 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: D 221 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7080 (mt-10) REVERT: E 4 GLU cc_start: 0.8491 (mp0) cc_final: 0.8219 (mp0) REVERT: E 45 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: E 221 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7011 (mt-10) REVERT: F 4 GLU cc_start: 0.8497 (mp0) cc_final: 0.8167 (mp0) REVERT: F 45 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: F 221 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7026 (mt-10) outliers start: 34 outliers final: 16 residues processed: 192 average time/residue: 0.7200 time to fit residues: 151.9082 Evaluate side-chains 191 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 314 VAL 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 198 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 17 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 182 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 165 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 186 optimal weight: 3.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100119 restraints weight = 19587.362| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.27 r_work: 0.3091 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1627 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= 0.164 Angle : 0.520 4.298 23130 Z= 0.288 Chirality : 0.047 0.132 2664 Planarity : 0.003 0.041 2937 Dihedral : 7.250 58.779 2325 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.62 % Allowed : 14.67 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2070 helix: 0.77 (0.23), residues: 540 sheet: 0.84 (0.30), residues: 294 loop : -0.23 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.012 0.001 TYR F 226 PHE 0.017 0.002 PHE A 16 TRP 0.006 0.001 TRP C 333 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00367 (17025) covalent geometry : angle 0.51983 (23130) hydrogen bonds : bond 0.04626 ( 594) hydrogen bonds : angle 5.40206 ( 1683) *********************** 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 199 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.661 Fit side-chains REVERT: A 139 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7988 (ttm-80) REVERT: A 265 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: B 139 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7933 (ttm-80) REVERT: D 4 GLU cc_start: 0.8468 (mp0) cc_final: 0.8142 (mp0) REVERT: D 45 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: D 146 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: D 221 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7078 (mt-10) REVERT: E 4 GLU cc_start: 0.8488 (mp0) cc_final: 0.8185 (mp0) REVERT: E 45 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: E 221 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7000 (mt-10) REVERT: F 4 GLU cc_start: 0.8488 (mp0) cc_final: 0.8175 (mp0) REVERT: F 45 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: F 221 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7057 (mt-10) outliers start: 30 outliers final: 14 residues processed: 192 average time/residue: 0.7051 time to fit residues: 148.6874 Evaluate side-chains 188 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 B residue 139 ARG Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 314 VAL 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 198 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 165 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 0.0060 chunk 201 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 0.0770 overall best weight: 3.2160 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.129077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102204 restraints weight = 19773.127| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.28 r_work: 0.3130 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1869 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= 0.103 Angle : 0.462 4.704 23130 Z= 0.256 Chirality : 0.045 0.133 2664 Planarity : 0.003 0.041 2937 Dihedral : 6.943 59.852 2325 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.62 % Allowed : 14.46 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2070 helix: 0.91 (0.24), residues: 540 sheet: 1.09 (0.29), residues: 294 loop : -0.15 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 127 TYR 0.010 0.001 TYR F 226 PHE 0.011 0.001 PHE B 16 TRP 0.008 0.001 TRP B 333 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00225 (17025) covalent geometry : angle 0.46171 (23130) hydrogen bonds : bond 0.03747 ( 594) hydrogen bonds : angle 5.10759 ( 1683) *********************** 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 198 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.630 Fit side-chains REVERT: A 265 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8001 (pp20) REVERT: C 265 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8069 (pp20) REVERT: D 4 GLU cc_start: 0.8435 (mp0) cc_final: 0.8123 (mp0) REVERT: D 45 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: E 4 GLU cc_start: 0.8485 (mp0) cc_final: 0.8171 (mp0) REVERT: E 45 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: F 1 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7511 (mmm) REVERT: F 4 GLU cc_start: 0.8480 (mp0) cc_final: 0.8211 (mp0) REVERT: F 45 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7911 (tm-30) outliers start: 30 outliers final: 12 residues processed: 191 average time/residue: 0.6722 time to fit residues: 141.8324 Evaluate side-chains 184 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 97 ILE 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 D residue 45 GLU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 1 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 111 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 147 optimal weight: 0.0060 chunk 27 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN D 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101508 restraints weight = 19766.889| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.28 r_work: 0.3115 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17025 Z= 0.117 Angle : 0.475 5.077 23130 Z= 0.263 Chirality : 0.045 0.134 2664 Planarity : 0.003 0.042 2937 Dihedral : 6.999 59.876 2325 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.46 % Allowed : 14.62 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2070 helix: 0.91 (0.24), residues: 540 sheet: 1.12 (0.29), residues: 294 loop : -0.15 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 139 TYR 0.012 0.001 TYR F 226 PHE 0.012 0.001 PHE A 16 TRP 0.007 0.001 TRP B 333 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00258 (17025) covalent geometry : angle 0.47527 (23130) hydrogen bonds : bond 0.03965 ( 594) hydrogen bonds : angle 5.15460 ( 1683) *********************** 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 195 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.737 Fit side-chains REVERT: A 265 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8022 (pp20) REVERT: C 265 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8105 (pp20) REVERT: D 4 GLU cc_start: 0.8462 (mp0) cc_final: 0.8146 (mp0) REVERT: D 45 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: E 4 GLU cc_start: 0.8492 (mp0) cc_final: 0.8164 (mp0) REVERT: E 45 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: E 221 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7040 (tp30) REVERT: F 1 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7526 (mmm) REVERT: F 4 GLU cc_start: 0.8492 (mp0) cc_final: 0.8191 (mp0) REVERT: F 45 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7921 (tm-30) outliers start: 27 outliers final: 12 residues processed: 190 average time/residue: 0.6760 time to fit residues: 141.5412 Evaluate side-chains 182 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 314 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 1 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 14 optimal weight: 30.0000 chunk 117 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 79 optimal weight: 0.0040 chunk 21 optimal weight: 5.9990 chunk 134 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 147 optimal weight: 0.3980 chunk 108 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 overall best weight: 4.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101624 restraints weight = 19639.067| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.28 r_work: 0.3118 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17025 Z= 0.115 Angle : 0.477 5.603 23130 Z= 0.263 Chirality : 0.045 0.133 2664 Planarity : 0.003 0.041 2937 Dihedral : 6.979 59.721 2325 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.13 % Allowed : 15.05 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 2070 helix: 0.91 (0.24), residues: 540 sheet: 1.15 (0.29), residues: 294 loop : -0.14 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 139 TYR 0.012 0.001 TYR F 226 PHE 0.012 0.001 PHE A 16 TRP 0.007 0.001 TRP B 333 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00255 (17025) covalent geometry : angle 0.47723 (23130) hydrogen bonds : bond 0.03910 ( 594) hydrogen bonds : angle 5.13951 ( 1683) ********************** 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 187 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.594 Fit side-chains REVERT: A 265 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8018 (pp20) REVERT: C 265 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8097 (pp20) REVERT: D 4 GLU cc_start: 0.8460 (mp0) cc_final: 0.8141 (mp0) REVERT: D 45 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: E 4 GLU cc_start: 0.8489 (mp0) cc_final: 0.8161 (mp0) REVERT: E 45 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: E 221 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7019 (tp30) REVERT: F 1 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7521 (mmm) REVERT: F 4 GLU cc_start: 0.8493 (mp0) cc_final: 0.8192 (mp0) REVERT: F 45 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7910 (tm-30) outliers start: 21 outliers final: 13 residues processed: 184 average time/residue: 0.6461 time to fit residues: 131.7236 Evaluate side-chains 184 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 314 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 1 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 41 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099775 restraints weight = 19618.685| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.28 r_work: 0.3083 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17025 Z= 0.189 Angle : 0.549 5.316 23130 Z= 0.304 Chirality : 0.048 0.154 2664 Planarity : 0.003 0.042 2937 Dihedral : 7.319 58.635 2325 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.29 % Allowed : 15.05 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 2070 helix: 0.75 (0.24), residues: 540 sheet: 0.89 (0.30), residues: 294 loop : -0.20 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 139 TYR 0.013 0.002 TYR F 226 PHE 0.018 0.002 PHE A 16 TRP 0.006 0.001 TRP D 87 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00426 (17025) covalent geometry : angle 0.54906 (23130) hydrogen bonds : bond 0.04843 ( 594) hydrogen bonds : angle 5.44841 ( 1683) =============================================================================== Job complete usr+sys time: 8341.22 seconds wall clock time: 142 minutes 11.81 seconds (8531.81 seconds total)