Starting phenix.real_space_refine on Sat Sep 12 16:53:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n06_24101/09_2026/7n06_24101.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n06_24101/09_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_24101/09_2026/7n06_24101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n06_24101/09_2026/7n06_24101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n06_24101/09_2026/7n06_24101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n06_24101/09_2026/7n06_24101.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7n06_24101/09_2026/7n06_24101.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n06_24101/09_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-2.2.1-6174/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, 'RNAv2': 2} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 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, 'RNAv2': 2} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 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, 'RNAv2': 2} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 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, 'RNAv2': 1} Modifications used: {'5*END': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 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, 'RNAv2': 1} Modifications used: {'5*END': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 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, 'RNAv2': 1} Modifications used: {'5*END': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 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: 4.01, per 1000 atoms: 0.23 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: 1.28 Conformation dependent library (CDL) restraints added in 665.9 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: 0.43 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: 2.90 Time building geometry restraints manager: 1.70 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: 21551 1.17 - 2.33: 1289 2.33 - 3.50: 180 3.50 - 4.66: 53 4.66 - 5.83: 30 Bond angle restraints: 23103 Sorted by residual: angle pdb=" O3' A I 400 " pdb=" C3' A I 400 " pdb=" C2' A I 400 " ideal model delta sigma weight residual 113.80 108.38 5.42 2.00e+00 2.50e-01 7.33e+00 angle pdb=" O3' A G 400 " pdb=" C3' A G 400 " pdb=" C2' A G 400 " ideal model delta sigma weight residual 113.80 108.54 5.26 2.00e+00 2.50e-01 6.91e+00 angle pdb=" O3' A H 400 " pdb=" C3' A H 400 " pdb=" C2' A H 400 " ideal model delta sigma weight residual 113.80 108.59 5.21 2.00e+00 2.50e-01 6.79e+00 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 ... (remaining 23098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 9305 17.89 - 35.78: 595 35.78 - 53.67: 132 53.67 - 71.56: 69 71.56 - 89.45: 48 Dihedral angle restraints: 10149 sinusoidal: 4107 harmonic: 6042 Sorted by residual: dihedral pdb=" C4' U L 401 " pdb=" C3' U L 401 " pdb=" C2' U L 401 " pdb=" C1' U L 401 " ideal model delta sinusoidal sigma weight residual 36.34 -37.61 73.96 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' U K 401 " pdb=" C3' U K 401 " pdb=" C2' U K 401 " pdb=" C1' U K 401 " ideal model delta sinusoidal sigma weight residual 36.35 -37.19 73.54 1 3.10e+00 1.04e-01 7.16e+02 dihedral pdb=" C4' U J 401 " pdb=" C3' U J 401 " pdb=" C2' U J 401 " pdb=" C1' U J 401 " ideal model delta sinusoidal sigma weight residual 36.34 -36.97 73.31 1 3.10e+00 1.04e-01 7.12e+02 ... (remaining 10146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1958 0.058 - 0.115: 617 0.115 - 0.173: 65 0.173 - 0.230: 3 0.230 - 0.288: 21 Chirality restraints: 2664 Sorted by residual: chirality pdb=" C2' U J 401 " pdb=" C3' U J 401 " pdb=" O2' U J 401 " pdb=" C1' U J 401 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' U K 401 " pdb=" C3' U K 401 " pdb=" O2' U K 401 " pdb=" C1' U K 401 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' U L 401 " pdb=" C4' U L 401 " pdb=" O3' U L 401 " pdb=" C2' U L 401 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 2661 not shown) Planarity restraints: 2937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 118 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO C 119 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 118 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 119 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 118 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO B 119 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.021 5.00e-02 4.00e+02 ... (remaining 2934 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 406 2.66 - 3.22: 16018 3.22 - 3.78: 29120 3.78 - 4.34: 42668 4.34 - 4.90: 63951 Nonbonded interactions: 152163 Sorted by model distance: nonbonded pdb=" OE1 GLU B 4 " pdb=" O HOH B 401 " model vdw 2.096 3.040 nonbonded pdb=" OE1 GLU C 4 " pdb=" O HOH C 401 " model vdw 2.097 3.040 nonbonded pdb=" OE1 GLU A 4 " pdb=" O HOH A 401 " model vdw 2.099 3.040 nonbonded pdb=" OD1 ASP F 92 " pdb=" O HOH F 401 " model vdw 2.106 3.040 nonbonded pdb=" OD1 ASP D 92 " pdb=" O HOH D 401 " model vdw 2.106 3.040 ... (remaining 152158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 401 through 402) selection = (chain 'H' and resid 401 through 402) selection = (chain 'I' and resid 401 through 402) selection = (chain 'J' and resid 401 through 402) selection = (chain 'K' and resid 401 through 402) selection = (chain 'L' and resid 401 through 402) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.010 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.510 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- 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= 0.324 Angle : 0.658 5.826 23103 Z= 0.352 Chirality : 0.057 0.288 2664 Planarity : 0.004 0.038 2937 Dihedral : 15.275 89.453 6249 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 0.00746 / 0.32 (17025) covalent geometry : angle 0.65771 / 0.35 (23103) 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 : 0.776 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: 0.7476 time to fit residues: 211.4252 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 : 0.727 ------------------------------------------------------------------------------- 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 245 GLN A 338 HIS B 245 GLN B 338 HIS C 245 GLN C 338 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099972 restraints weight = 19343.327| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.35 r_work: 0.3095 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- 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 = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1408 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= 0.159 Angle : 0.635 11.934 23103 Z= 0.322 Chirality : 0.057 0.555 2664 Planarity : 0.003 0.026 2937 Dihedral : 9.525 133.812 2320 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.05 % Allowed : 11.33 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.37 (0.17), residues: 2070 helix: 0.06 (0.22), residues: 540 sheet: 0.49 (0.30), residues: 294 loop : -0.52 (0.16), residues: 1236 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 0.020 0.002 PHE B 16 TRP 0.007 0.001 TRP B 333 HIS 0.020 0.002 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (17025) covalent geometry : angle 0.63523 / 0.32 (23103) hydrogen bonds : bond 0.05001 / 3.36 ( 594) hydrogen bonds : angle 5.92779 / 4.14 ( 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 224 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.580 Fit side-chains REVERT: A 245 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8838 (tp-100) REVERT: A 265 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: B 245 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8857 (tp40) REVERT: B 265 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8313 (tm-30) REVERT: C 245 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8845 (tp40) REVERT: C 265 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8112 (pp20) REVERT: D 45 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: D 225 ARG cc_start: 0.6898 (ttm170) cc_final: 0.6593 (ttm-80) REVERT: E 45 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: F 45 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: F 225 ARG cc_start: 0.6852 (ttm170) cc_final: 0.6546 (ttm-80) outliers start: 38 outliers final: 12 residues processed: 207 average time/residue: 0.7319 time to fit residues: 166.6222 Evaluate side-chains 191 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 245 GLN 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: 30.0000 chunk 177 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 153 optimal weight: 0.0980 chunk 146 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN A 245 GLN B 245 GLN C 200 ASN C 245 GLN C 338 HIS F 20 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.131100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.102956 restraints weight = 19538.308| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.20 r_work: 0.3164 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1859 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= 0.093 Angle : 0.481 5.848 23103 Z= 0.257 Chirality : 0.047 0.259 2664 Planarity : 0.003 0.037 2937 Dihedral : 9.448 144.613 2302 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.78 % Allowed : 13.21 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.18), residues: 2070 helix: 0.74 (0.23), residues: 534 sheet: 0.76 (0.28), residues: 324 loop : -0.29 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 258 TYR 0.011 0.001 TYR D 226 PHE 0.009 0.001 PHE E 269 TRP 0.007 0.001 TRP A 333 HIS 0.008 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (17025) covalent geometry : angle 0.48064 / 0.26 (23103) hydrogen bonds : bond 0.03696 / 2.50 ( 594) hydrogen bonds : angle 5.23701 / 3.64 ( 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 220 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.778 Fit side-chains REVERT: B 115 THR cc_start: 0.9217 (t) cc_final: 0.9014 (m) REVERT: C 317 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7607 (pttp) REVERT: D 4 GLU cc_start: 0.8433 (mp0) cc_final: 0.8086 (mp0) REVERT: D 45 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: D 225 ARG cc_start: 0.6900 (ttm170) cc_final: 0.6667 (ttm-80) REVERT: E 4 GLU cc_start: 0.8442 (mp0) cc_final: 0.8043 (mp0) REVERT: E 45 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: F 1 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7359 (mmm) REVERT: F 4 GLU cc_start: 0.8440 (mp0) cc_final: 0.8099 (mp0) REVERT: F 45 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: F 225 ARG cc_start: 0.6888 (ttm170) cc_final: 0.6637 (ttm-80) outliers start: 33 outliers final: 10 residues processed: 208 average time/residue: 0.7042 time to fit residues: 161.8842 Evaluate side-chains 190 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 PHE 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 233 PHE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 45 GLU 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 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: 10.0000 chunk 38 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 116 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN B 245 GLN C 245 GLN C 338 HIS D 235 HIS E 235 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100663 restraints weight = 19347.129| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.17 r_work: 0.3127 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17025 Z= 0.138 Angle : 0.525 5.331 23103 Z= 0.282 Chirality : 0.049 0.272 2664 Planarity : 0.003 0.040 2937 Dihedral : 9.354 144.412 2292 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.89 % Allowed : 14.29 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2070 helix: 0.76 (0.24), residues: 540 sheet: 0.81 (0.30), residues: 294 loop : -0.24 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.013 0.001 TYR D 226 PHE 0.020 0.002 PHE F 233 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 0.00304 / 0.14 (17025) covalent geometry : angle 0.52457 / 0.28 (23103) hydrogen bonds : bond 0.04417 / 2.96 ( 594) hydrogen bonds : angle 5.33076 / 3.69 ( 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 214 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.898 Fit side-chains REVERT: B 139 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7901 (ttm-80) REVERT: D 4 GLU cc_start: 0.8441 (mp0) cc_final: 0.8131 (mp0) REVERT: D 45 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: D 225 ARG cc_start: 0.6966 (ttm170) cc_final: 0.6678 (ttm-80) REVERT: E 4 GLU cc_start: 0.8443 (mp0) cc_final: 0.8104 (mp0) REVERT: E 45 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: F 4 GLU cc_start: 0.8441 (mp0) cc_final: 0.8137 (mp0) REVERT: F 45 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: F 225 ARG cc_start: 0.6936 (ttm170) cc_final: 0.6631 (ttm-80) outliers start: 35 outliers final: 12 residues processed: 204 average time/residue: 0.6522 time to fit residues: 147.6582 Evaluate side-chains 181 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain C residue 97 ILE 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 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: 9.9990 chunk 191 optimal weight: 9.9990 chunk 34 optimal weight: 40.0000 chunk 165 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN B 245 GLN C 245 GLN C 338 HIS D 20 GLN D 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099873 restraints weight = 19305.742| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.17 r_work: 0.3113 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17025 Z= 0.166 Angle : 0.552 5.934 23103 Z= 0.296 Chirality : 0.050 0.332 2664 Planarity : 0.003 0.040 2937 Dihedral : 9.668 145.873 2292 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.37 % Allowed : 13.97 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2070 helix: 0.74 (0.23), residues: 540 sheet: 0.82 (0.30), residues: 294 loop : -0.25 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.013 0.001 TYR D 226 PHE 0.017 0.002 PHE A 16 TRP 0.005 0.001 TRP C 333 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (17025) covalent geometry : angle 0.55159 / 0.30 (23103) hydrogen bonds : bond 0.04678 / 3.14 ( 594) hydrogen bonds : angle 5.43891 / 3.78 ( 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 216 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.646 Fit side-chains REVERT: A 139 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7939 (ttm-80) REVERT: B 139 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7927 (ttm-80) REVERT: D 4 GLU cc_start: 0.8461 (mp0) cc_final: 0.8150 (mp0) REVERT: D 45 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: D 146 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7202 (mm-30) REVERT: E 4 GLU cc_start: 0.8463 (mp0) cc_final: 0.8168 (mp0) REVERT: E 45 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: E 146 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: E 221 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7024 (mt-10) REVERT: F 4 GLU cc_start: 0.8460 (mp0) cc_final: 0.8159 (mp0) REVERT: F 45 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: F 221 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7009 (mt-10) outliers start: 44 outliers final: 16 residues processed: 204 average time/residue: 0.7169 time to fit residues: 161.3732 Evaluate side-chains 191 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 220 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 185 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 84 optimal weight: 0.0050 chunk 144 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 161 optimal weight: 50.0000 chunk 115 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 85 optimal weight: 0.4980 overall best weight: 4.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN B 245 GLN C 245 GLN D 137 ASN D 200 ASN E 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.101227 restraints weight = 19343.854| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.15 r_work: 0.3142 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 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: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17025 Z= 0.121 Angle : 0.502 5.274 23103 Z= 0.271 Chirality : 0.048 0.259 2664 Planarity : 0.003 0.041 2937 Dihedral : 9.475 142.741 2292 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.78 % Allowed : 14.56 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 2070 helix: 0.83 (0.24), residues: 540 sheet: 1.02 (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 D 258 TYR 0.013 0.001 TYR F 226 PHE 0.013 0.001 PHE B 16 TRP 0.007 0.001 TRP C 333 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17025) covalent geometry : angle 0.50245 / 0.27 (23103) hydrogen bonds : bond 0.04063 / 2.74 ( 594) hydrogen bonds : angle 5.23048 / 3.62 ( 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 202 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.573 Fit side-chains REVERT: D 4 GLU cc_start: 0.8430 (mp0) cc_final: 0.8111 (mp0) REVERT: D 45 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: E 4 GLU cc_start: 0.8439 (mp0) cc_final: 0.8105 (mp0) REVERT: E 45 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: F 4 GLU cc_start: 0.8431 (mp0) cc_final: 0.8128 (mp0) REVERT: F 45 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7863 (tm-30) outliers start: 33 outliers final: 13 residues processed: 195 average time/residue: 0.7212 time to fit residues: 155.2068 Evaluate side-chains 181 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain 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 166 VAL Chi-restraints excluded: chain F residue 198 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 17 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 182 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 165 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 186 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN B 200 ASN B 245 GLN C 245 GLN D 137 ASN D 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099310 restraints weight = 19357.255| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.16 r_work: 0.3099 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 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 = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 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 : 0.004 0.036 17025 Z= 0.186 Angle : 0.573 6.691 23103 Z= 0.307 Chirality : 0.052 0.367 2664 Planarity : 0.003 0.042 2937 Dihedral : 9.871 145.687 2292 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.05 % Allowed : 14.29 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2070 helix: 0.69 (0.23), residues: 540 sheet: 0.84 (0.30), residues: 294 loop : -0.24 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.013 0.002 TYR F 226 PHE 0.018 0.002 PHE B 16 TRP 0.006 0.001 TRP D 87 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (17025) covalent geometry : angle 0.57305 / 0.31 (23103) hydrogen bonds : bond 0.04862 / 3.25 ( 594) hydrogen bonds : angle 5.47434 / 3.81 ( 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 206 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.719 Fit side-chains REVERT: A 139 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7939 (ttm-80) REVERT: B 139 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7929 (ttm-80) REVERT: D 4 GLU cc_start: 0.8460 (mp0) cc_final: 0.8138 (mp0) REVERT: D 45 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: D 146 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: D 221 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7043 (mt-10) REVERT: E 45 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: E 221 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7028 (mt-10) REVERT: F 45 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7968 (tm-30) outliers start: 38 outliers final: 15 residues processed: 196 average time/residue: 0.7331 time to fit residues: 158.1630 Evaluate side-chains 187 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG 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 220 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 319 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 165 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 105 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN B 245 GLN C 245 GLN C 338 HIS D 137 ASN D 200 ASN F 200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101625 restraints weight = 19471.491| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.20 r_work: 0.3139 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- 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: 3 | |-----------------------------------------------------------------------------| |-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: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17025 Z= 0.118 Angle : 0.499 5.333 23103 Z= 0.269 Chirality : 0.048 0.254 2664 Planarity : 0.003 0.041 2937 Dihedral : 9.621 141.883 2292 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.56 % Allowed : 14.67 % Favored : 83.76 % 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 (0.18), residues: 2070 helix: 0.84 (0.24), residues: 540 sheet: 1.05 (0.29), residues: 294 loop : -0.16 (0.17), residues: 1236 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 0.012 0.001 PHE C 16 TRP 0.007 0.001 TRP A 333 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17025) covalent geometry : angle 0.49860 / 0.27 (23103) hydrogen bonds : bond 0.03977 / 2.68 ( 594) hydrogen bonds : angle 5.19426 / 3.60 ( 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 199 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.735 Fit side-chains REVERT: A 265 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7976 (pp20) REVERT: D 4 GLU cc_start: 0.8426 (mp0) cc_final: 0.8130 (mp0) REVERT: D 45 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: E 4 GLU cc_start: 0.8454 (mp0) cc_final: 0.8150 (mp0) REVERT: E 45 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: F 4 GLU cc_start: 0.8452 (mp0) cc_final: 0.8175 (mp0) REVERT: F 45 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7839 (tm-30) outliers start: 29 outliers final: 14 residues processed: 192 average time/residue: 0.6868 time to fit residues: 145.9546 Evaluate side-chains 181 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 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 1 MET Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 111 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 147 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 202 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN B 200 ASN B 245 GLN C 245 GLN D 137 ASN D 200 ASN F 200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101471 restraints weight = 19568.805| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.24 r_work: 0.3130 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17025 Z= 0.121 Angle : 0.502 5.491 23103 Z= 0.271 Chirality : 0.048 0.257 2664 Planarity : 0.003 0.042 2937 Dihedral : 9.694 142.532 2292 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.51 % Allowed : 14.62 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.40 (0.18), residues: 2070 helix: 0.85 (0.24), residues: 540 sheet: 1.10 (0.29), residues: 294 loop : -0.15 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 139 TYR 0.011 0.001 TYR F 226 PHE 0.013 0.001 PHE A 16 TRP 0.007 0.001 TRP C 333 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (17025) covalent geometry : angle 0.50237 / 0.27 (23103) hydrogen bonds : bond 0.04021 / 2.70 ( 594) hydrogen bonds : angle 5.18312 / 3.59 ( 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 197 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.720 Fit side-chains REVERT: A 265 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8001 (pp20) REVERT: D 4 GLU cc_start: 0.8440 (mp0) cc_final: 0.8136 (mp0) REVERT: D 45 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: E 4 GLU cc_start: 0.8455 (mp0) cc_final: 0.8143 (mp0) REVERT: E 45 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: E 221 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7020 (tp30) REVERT: F 4 GLU cc_start: 0.8456 (mp0) cc_final: 0.8169 (mp0) REVERT: F 45 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7861 (tm-30) outliers start: 28 outliers final: 14 residues processed: 191 average time/residue: 0.6837 time to fit residues: 143.9871 Evaluate side-chains 183 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 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 1 MET Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 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: 0.8980 chunk 21 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN B 245 GLN C 245 GLN C 338 HIS D 137 ASN D 200 ASN F 200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100983 restraints weight = 19508.546| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.26 r_work: 0.3114 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17025 Z= 0.138 Angle : 0.524 5.723 23103 Z= 0.282 Chirality : 0.049 0.283 2664 Planarity : 0.003 0.042 2937 Dihedral : 9.808 143.351 2292 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.29 % Allowed : 14.94 % Favored : 83.76 % 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: 0.37 (0.18), residues: 2070 helix: 0.81 (0.24), residues: 540 sheet: 1.09 (0.29), residues: 294 loop : -0.17 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 139 TYR 0.012 0.001 TYR F 226 PHE 0.014 0.002 PHE B 16 TRP 0.006 0.001 TRP B 333 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (17025) covalent geometry : angle 0.52431 / 0.28 (23103) hydrogen bonds : bond 0.04252 / 2.86 ( 594) hydrogen bonds : angle 5.26496 / 3.65 ( 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 189 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.667 Fit side-chains REVERT: A 265 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7999 (pp20) REVERT: D 4 GLU cc_start: 0.8464 (mp0) cc_final: 0.8137 (mp0) REVERT: D 45 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: D 221 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7015 (tp30) REVERT: E 4 GLU cc_start: 0.8474 (mp0) cc_final: 0.8175 (mp0) REVERT: E 45 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: E 221 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7027 (tp30) REVERT: F 4 GLU cc_start: 0.8470 (mp0) cc_final: 0.8175 (mp0) REVERT: F 45 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7876 (tm-30) outliers start: 24 outliers final: 13 residues processed: 184 average time/residue: 0.6700 time to fit residues: 136.2427 Evaluate side-chains 181 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 41 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN B 200 ASN B 245 GLN C 245 GLN D 137 ASN D 200 ASN F 200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100887 restraints weight = 19681.808| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.27 r_work: 0.3110 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17025 Z= 0.139 Angle : 0.524 5.735 23103 Z= 0.281 Chirality : 0.049 0.285 2664 Planarity : 0.003 0.042 2937 Dihedral : 9.833 143.032 2292 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.24 % Allowed : 14.94 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.18), residues: 2070 helix: 0.80 (0.24), residues: 540 sheet: 1.10 (0.29), residues: 294 loop : -0.17 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 139 TYR 0.012 0.001 TYR F 226 PHE 0.014 0.002 PHE B 16 TRP 0.006 0.001 TRP B 333 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (17025) covalent geometry : angle 0.52376 / 0.28 (23103) hydrogen bonds : bond 0.04255 / 2.86 ( 594) hydrogen bonds : angle 5.25990 / 3.65 ( 1683) =============================================================================== Job complete usr+sys time: 8621.42 seconds wall clock time: 147 minutes 19.25 seconds (8839.25 seconds total)