Starting phenix.real_space_refine on Sat Jul 4 00:15:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n06_24101/07_2026/7n06_24101.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n06_24101/07_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_24101/07_2026/7n06_24101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n06_24101/07_2026/7n06_24101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n06_24101/07_2026/7n06_24101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n06_24101/07_2026/7n06_24101.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7n06_24101/07_2026/7n06_24101.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n06_24101/07_2026/7n06_24101.cif" } 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-6108/lib/python3.11/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: 3.42, per 1000 atoms: 0.20 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 712.7 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: 0.58 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: 2.72 Time building geometry restraints manager: 1.95 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: 9354 17.89 - 35.78: 585 35.78 - 53.67: 132 53.67 - 71.56: 45 71.56 - 89.45: 42 Dihedral angle restraints: 10158 sinusoidal: 4116 harmonic: 6042 Sorted by residual: dihedral pdb=" CA PHE A 177 " pdb=" C PHE A 177 " pdb=" N ASN A 178 " pdb=" CA ASN A 178 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE B 177 " pdb=" C PHE B 177 " pdb=" N ASN B 178 " pdb=" CA ASN B 178 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE C 177 " pdb=" C PHE C 177 " pdb=" N ASN C 178 " pdb=" CA ASN C 178 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 10155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1267 0.033 - 0.067: 880 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: 0.04 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.290 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 17025 Z= 0.323 Angle : 0.629 5.826 23130 Z= 0.345 Chirality : 0.051 0.167 2664 Planarity : 0.004 0.038 2937 Dihedral : 14.548 89.453 6258 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.39 % Rotamer: Outliers : 2.10 % 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/Z covalent geometry : bond 0.00745 / 0.32 (17025) covalent geometry : angle 0.62942 / 0.35 (23130) hydrogen bonds : bond 0.20006 / 13.07 ( 594) hydrogen bonds : angle 8.02381 / 5.61 ( 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 : 0.499 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: 0.6834 time to fit residues: 193.4037 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 : 0.668 ------------------------------------------------------------------------------- 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... A 338 HIS B 338 HIS C 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100413 restraints weight = 19638.003| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.22 r_work: 0.3105 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17025 Z= 0.153 Angle : 0.533 4.414 23130 Z= 0.296 Chirality : 0.047 0.134 2664 Planarity : 0.003 0.026 2937 Dihedral : 7.500 64.021 2329 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.78 % Allowed : 11.65 % Favored : 86.57 % 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: 0.12 (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 0.004 0.000 ARG D 258 TYR 0.011 0.001 TYR F 226 PHE 0.019 0.002 PHE C 16 TRP 0.008 0.001 TRP B 333 HIS 0.018 0.002 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (17025) covalent geometry : angle 0.53272 / 0.30 (23130) hydrogen bonds : bond 0.05004 / 3.36 ( 594) hydrogen bonds : angle 5.90731 / 4.13 ( 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 221 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.738 Fit side-chains REVERT: A 265 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: B 265 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: C 265 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8119 (pp20) REVERT: D 45 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: D 225 ARG cc_start: 0.6937 (ttm170) cc_final: 0.6628 (ttm-80) REVERT: E 45 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: F 45 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: F 225 ARG cc_start: 0.6895 (ttm170) cc_final: 0.6585 (ttm-80) outliers start: 33 outliers final: 11 residues processed: 205 average time/residue: 0.6390 time to fit residues: 144.1751 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 : 0.650 ------------------------------------------------------------------------------- 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: 40.0000 chunk 72 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 177 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 153 optimal weight: 0.1980 chunk 146 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN C 200 ASN C 338 HIS F 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101849 restraints weight = 20004.049| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.23 r_work: 0.3134 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1680 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 : 0.469 3.961 23130 Z= 0.259 Chirality : 0.045 0.134 2664 Planarity : 0.003 0.037 2937 Dihedral : 6.707 59.484 2311 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 0.13 (0.18), residues: 2070 helix: 0.65 (0.23), residues: 540 sheet: 0.74 (0.28), residues: 324 loop : -0.31 (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 C 333 HIS 0.008 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (17025) covalent geometry : angle 0.46866 / 0.26 (23130) hydrogen bonds : bond 0.04045 / 2.72 ( 594) hydrogen bonds : angle 5.31888 / 3.69 ( 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 217 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.618 Fit side-chains REVERT: C 317 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7618 (pttp) REVERT: D 4 GLU cc_start: 0.8456 (mp0) cc_final: 0.8090 (mp0) REVERT: D 45 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: D 225 ARG cc_start: 0.6941 (ttm170) cc_final: 0.6710 (ttm-80) REVERT: E 4 GLU cc_start: 0.8465 (mp0) cc_final: 0.8178 (mp0) REVERT: E 45 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: F 1 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7406 (mmm) REVERT: F 4 GLU cc_start: 0.8467 (mp0) cc_final: 0.8243 (mp0) REVERT: F 45 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: F 221 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6980 (mt-10) REVERT: F 225 ARG cc_start: 0.6909 (ttm170) cc_final: 0.6663 (ttm-80) outliers start: 32 outliers final: 10 residues processed: 205 average time/residue: 0.6225 time to fit residues: 141.8082 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 : 0.656 ------------------------------------------------------------------------------- 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: 8.9990 chunk 4 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 169 optimal weight: 0.4980 chunk 110 optimal weight: 0.6980 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3721 r_free = 0.3721 target = 0.128489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101281 restraints weight = 19794.873| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.23 r_work: 0.3122 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17025 Z= 0.126 Angle : 0.484 4.596 23130 Z= 0.268 Chirality : 0.046 0.134 2664 Planarity : 0.003 0.040 2937 Dihedral : 6.144 58.971 2301 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.89 % Allowed : 14.19 % 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: 0.23 (0.18), residues: 2070 helix: 0.79 (0.24), residues: 540 sheet: 0.83 (0.30), residues: 294 loop : -0.25 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.014 0.001 TYR F 226 PHE 0.015 0.001 PHE A 16 TRP 0.006 0.001 TRP B 333 HIS 0.008 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (17025) covalent geometry : angle 0.48441 / 0.27 (23130) hydrogen bonds : bond 0.04214 / 2.84 ( 594) hydrogen bonds : angle 5.27436 / 3.66 ( 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 213 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.725 Fit side-chains REVERT: B 139 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7912 (ttm-80) REVERT: D 4 GLU cc_start: 0.8449 (mp0) cc_final: 0.8135 (mp0) REVERT: D 45 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: D 225 ARG cc_start: 0.6971 (ttm170) cc_final: 0.6700 (ttm-80) REVERT: E 4 GLU cc_start: 0.8466 (mp0) cc_final: 0.8125 (mp0) REVERT: E 45 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: F 1 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7426 (mmm) REVERT: F 4 GLU cc_start: 0.8465 (mp0) cc_final: 0.8154 (mp0) REVERT: F 45 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: F 221 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6980 (mt-10) outliers start: 35 outliers final: 12 residues processed: 204 average time/residue: 0.6084 time to fit residues: 137.7908 Evaluate side-chains 190 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 166 VAL 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: 0.7980 chunk 191 optimal weight: 5.9990 chunk 34 optimal weight: 40.0000 chunk 165 optimal weight: 40.0000 chunk 105 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 157 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 338 HIS D 137 ASN E 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101562 restraints weight = 19740.710| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.23 r_work: 0.3129 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17025 Z= 0.119 Angle : 0.474 3.997 23130 Z= 0.263 Chirality : 0.045 0.133 2664 Planarity : 0.003 0.041 2937 Dihedral : 6.080 59.896 2301 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 14.72 % Favored : 83.50 % 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: 0.33 (0.18), residues: 2070 helix: 0.86 (0.24), residues: 540 sheet: 1.01 (0.29), residues: 294 loop : -0.22 (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 0.013 0.001 PHE A 16 TRP 0.006 0.001 TRP C 333 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (17025) covalent geometry : angle 0.47398 / 0.26 (23130) hydrogen bonds : bond 0.04040 / 2.72 ( 594) hydrogen bonds : angle 5.20375 / 3.60 ( 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 208 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.700 Fit side-chains REVERT: D 4 GLU cc_start: 0.8437 (mp0) cc_final: 0.8100 (mp0) REVERT: D 45 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: E 4 GLU cc_start: 0.8457 (mp0) cc_final: 0.8100 (mp0) REVERT: E 45 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: F 1 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7428 (mmm) REVERT: F 4 GLU cc_start: 0.8452 (mp0) cc_final: 0.8124 (mp0) REVERT: F 45 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: F 221 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7015 (mt-10) outliers start: 33 outliers final: 13 residues processed: 196 average time/residue: 0.6624 time to fit residues: 143.8019 Evaluate side-chains 186 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 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 198 SER 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: 4.9990 chunk 78 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 161 optimal weight: 50.0000 chunk 115 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 20 GLN D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100381 restraints weight = 19646.549| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.29 r_work: 0.3093 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1665 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= 0.150 Angle : 0.506 4.136 23130 Z= 0.281 Chirality : 0.047 0.133 2664 Planarity : 0.003 0.042 2937 Dihedral : 6.219 58.637 2301 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.28 (0.18), residues: 2070 helix: 0.79 (0.24), residues: 540 sheet: 1.01 (0.32), residues: 264 loop : -0.22 (0.17), residues: 1266 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 0.016 0.002 PHE A 16 TRP 0.006 0.001 TRP C 333 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (17025) covalent geometry : angle 0.50624 / 0.28 (23130) hydrogen bonds : bond 0.04480 / 3.01 ( 594) hydrogen bonds : angle 5.34376 / 3.71 ( 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 : 0.764 Fit side-chains REVERT: A 139 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7989 (ttm-80) REVERT: B 139 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7958 (ttm-80) REVERT: D 4 GLU cc_start: 0.8481 (mp0) cc_final: 0.8139 (mp0) REVERT: D 45 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: E 4 GLU cc_start: 0.8495 (mp0) cc_final: 0.8222 (mp0) REVERT: E 45 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: E 47 LYS cc_start: 0.9241 (mmmm) cc_final: 0.9030 (mmmm) REVERT: E 146 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: F 4 GLU cc_start: 0.8501 (mp0) cc_final: 0.8170 (mp0) REVERT: F 45 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: F 221 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7020 (mt-10) outliers start: 34 outliers final: 16 residues processed: 192 average time/residue: 0.6784 time to fit residues: 143.7096 Evaluate side-chains 189 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 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: 20.0000 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 165 optimal weight: 40.0000 chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 186 optimal weight: 30.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3694 r_free = 0.3694 target = 0.126661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099393 restraints weight = 19577.665| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.28 r_work: 0.3074 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 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 = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17025 Z= 0.204 Angle : 0.557 4.603 23130 Z= 0.309 Chirality : 0.049 0.160 2664 Planarity : 0.004 0.041 2937 Dihedral : 6.423 57.182 2301 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.78 % Allowed : 14.67 % Favored : 83.55 % 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: 0.17 (0.18), residues: 2070 helix: 0.67 (0.23), residues: 540 sheet: 0.82 (0.30), residues: 294 loop : -0.26 (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 0.019 0.002 PHE A 16 TRP 0.006 0.001 TRP E 87 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (17025) covalent geometry : angle 0.55651 / 0.31 (23130) hydrogen bonds : bond 0.05038 / 3.37 ( 594) hydrogen bonds : angle 5.53340 / 3.85 ( 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 201 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.741 Fit side-chains REVERT: A 139 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7981 (ttm-80) REVERT: A 265 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8031 (pp20) REVERT: B 139 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7960 (ttm-80) REVERT: D 45 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: D 146 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: E 45 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: E 146 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: E 221 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7013 (mt-10) REVERT: F 45 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: F 146 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: F 221 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6991 (mt-10) outliers start: 33 outliers final: 15 residues processed: 192 average time/residue: 0.6915 time to fit residues: 146.2800 Evaluate side-chains 188 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 146 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 146 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 SER 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: 8.9990 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 338 HIS D 137 ASN D 200 ASN F 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.128087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101022 restraints weight = 19725.234| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.28 r_work: 0.3110 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 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 = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17025 Z= 0.127 Angle : 0.487 4.842 23130 Z= 0.270 Chirality : 0.046 0.133 2664 Planarity : 0.003 0.042 2937 Dihedral : 6.161 59.626 2301 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.83 % Allowed : 14.24 % 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: 0.33 (0.18), residues: 2070 helix: 0.79 (0.24), residues: 540 sheet: 1.03 (0.29), residues: 294 loop : -0.19 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 139 TYR 0.011 0.001 TYR F 226 PHE 0.014 0.001 PHE C 16 TRP 0.007 0.001 TRP B 333 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (17025) covalent geometry : angle 0.48683 / 0.27 (23130) hydrogen bonds : bond 0.04175 / 2.81 ( 594) hydrogen bonds : angle 5.26954 / 3.65 ( 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 202 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.503 Fit side-chains REVERT: C 265 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8074 (pp20) REVERT: D 4 GLU cc_start: 0.8459 (mp0) cc_final: 0.8163 (mp0) REVERT: D 45 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: E 4 GLU cc_start: 0.8494 (mp0) cc_final: 0.8183 (mp0) REVERT: E 45 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: F 4 GLU cc_start: 0.8496 (mp0) cc_final: 0.8218 (mp0) REVERT: F 45 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7922 (tm-30) outliers start: 34 outliers final: 15 residues processed: 193 average time/residue: 0.6314 time to fit residues: 134.8404 Evaluate side-chains 183 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 GLU 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 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=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: 0.0670 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 overall best weight: 2.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3735 r_free = 0.3735 target = 0.129582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102697 restraints weight = 19770.223| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.27 r_work: 0.3138 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 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 = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1947 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 : 0.451 5.223 23130 Z= 0.250 Chirality : 0.045 0.133 2664 Planarity : 0.003 0.040 2937 Dihedral : 5.901 59.940 2301 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.97 % Allowed : 15.05 % Favored : 83.98 % 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: 0.90 (0.24), residues: 540 sheet: 1.16 (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 0.010 0.001 TYR F 226 PHE 0.010 0.001 PHE A 16 TRP 0.008 0.001 TRP B 333 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (17025) covalent geometry : angle 0.45111 / 0.25 (23130) hydrogen bonds : bond 0.03549 / 2.40 ( 594) hydrogen bonds : angle 5.03459 / 3.48 ( 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 188 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.730 Fit side-chains REVERT: C 265 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8109 (pp20) REVERT: D 4 GLU cc_start: 0.8437 (mp0) cc_final: 0.8155 (mp0) REVERT: D 45 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: E 4 GLU cc_start: 0.8482 (mp0) cc_final: 0.8183 (mp0) REVERT: E 45 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: F 1 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7502 (mmm) REVERT: F 4 GLU cc_start: 0.8479 (mp0) cc_final: 0.8228 (mp0) REVERT: F 45 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7913 (tm-30) outliers start: 18 outliers final: 7 residues processed: 185 average time/residue: 0.6927 time to fit residues: 141.6313 Evaluate side-chains 178 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 D residue 45 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 148 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 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: 7.9990 chunk 79 optimal weight: 0.0060 chunk 21 optimal weight: 8.9990 chunk 134 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 chunk 147 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 overall best weight: 2.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.102863 restraints weight = 19692.886| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.27 r_work: 0.3139 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 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 = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17025 Z= 0.094 Angle : 0.450 5.450 23130 Z= 0.248 Chirality : 0.044 0.133 2664 Planarity : 0.003 0.040 2937 Dihedral : 5.775 59.792 2299 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.81 % Allowed : 15.59 % Favored : 83.60 % 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: 0.51 (0.18), residues: 2070 helix: 1.02 (0.24), residues: 534 sheet: 1.21 (0.29), residues: 294 loop : -0.13 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 139 TYR 0.011 0.001 TYR F 226 PHE 0.010 0.001 PHE B 16 TRP 0.009 0.001 TRP B 333 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (17025) covalent geometry : angle 0.44969 / 0.25 (23130) hydrogen bonds : bond 0.03473 / 2.35 ( 594) hydrogen bonds : angle 4.97706 / 3.44 ( 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 184 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.779 Fit side-chains REVERT: C 265 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8116 (pp20) REVERT: D 4 GLU cc_start: 0.8440 (mp0) cc_final: 0.8151 (mp0) REVERT: D 45 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: E 4 GLU cc_start: 0.8485 (mp0) cc_final: 0.8181 (mp0) REVERT: E 45 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: F 1 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7497 (mmm) REVERT: F 4 GLU cc_start: 0.8480 (mp0) cc_final: 0.8219 (mp0) REVERT: F 45 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7921 (tm-30) outliers start: 15 outliers final: 9 residues processed: 180 average time/residue: 0.5975 time to fit residues: 119.6949 Evaluate side-chains 181 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 41 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 40.0000 chunk 114 optimal weight: 7.9990 chunk 17 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.128338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101185 restraints weight = 19643.089| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.26 r_work: 0.3112 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.97 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 = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 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 0.030 17025 Z= 0.131 Angle : 0.488 5.688 23130 Z= 0.270 Chirality : 0.046 0.132 2664 Planarity : 0.003 0.041 2937 Dihedral : 5.945 59.556 2298 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.13 % Allowed : 15.32 % Favored : 83.55 % 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: 0.87 (0.24), residues: 540 sheet: 1.19 (0.29), residues: 294 loop : -0.16 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 139 TYR 0.013 0.001 TYR E 226 PHE 0.014 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/Z covalent geometry : bond 0.00290 / 0.13 (17025) covalent geometry : angle 0.48784 / 0.27 (23130) hydrogen bonds : bond 0.04096 / 2.75 ( 594) hydrogen bonds : angle 5.17581 / 3.59 ( 1683) =============================================================================== Job complete usr+sys time: 7851.20 seconds wall clock time: 134 minutes 12.06 seconds (8052.06 seconds total)