Starting phenix.real_space_refine on Mon Apr 6 00:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rgn_53951/04_2026/9rgn_53951.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rgn_53951/04_2026/9rgn_53951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rgn_53951/04_2026/9rgn_53951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rgn_53951/04_2026/9rgn_53951.map" model { file = "/net/cci-nas-00/data/ceres_data/9rgn_53951/04_2026/9rgn_53951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rgn_53951/04_2026/9rgn_53951.cif" } resolution = 3.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.005 sd= 0.110 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: 4 Type Number sf(0) Gaussians S 85 5.16 5 C 9340 2.51 5 N 2306 2.21 5 O 2525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14256 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2794 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2848 Conformer: "C" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2848 Chain: "B" Number of atoms: 2788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2848 Chain: "C" Number of atoms: 2788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2848 Chain: "D" Number of atoms: 2788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2848 Chain: "E" Number of atoms: 2788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 331, 2782 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2848 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'IVM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.02, per 1000 atoms: 0.42 Number of scatterers: 14256 At special positions: 0 Unit cell: (93.677, 92.019, 125.179, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 85 16.00 O 2525 8.00 N 2306 7.00 C 9340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 115 " distance=2.08 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 145 " distance=2.12 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 115 " distance=2.08 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 145 " distance=2.12 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 115 " distance=2.08 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 145 " distance=2.12 Simple disulfide: pdb=" SG CYS D 69 " - pdb=" SG CYS D 115 " distance=2.08 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 145 " distance=2.12 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS E 115 " distance=2.08 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 145 " distance=2.12 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: 1.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 38.7% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 removed outlier: 3.934A pdb=" N LEU A 19 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.551A pdb=" N GLU A 82 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 134 through 138 removed outlier: 4.636A pdb=" N ASN A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 220 through 233 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 241 through 261 removed outlier: 3.547A pdb=" N THR A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 302 removed outlier: 3.660A pdb=" N LEU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 333 removed outlier: 3.957A pdb=" N TYR A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Proline residue: A 321 - end of helix Processing helix chain 'B' and resid 14 through 20 removed outlier: 3.934A pdb=" N LEU B 19 " --> pdb=" O THR B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.551A pdb=" N GLU B 82 " --> pdb=" O HIS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 134 through 138 removed outlier: 4.636A pdb=" N ASN B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 220 through 233 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 241 through 261 removed outlier: 3.548A pdb=" N THR B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 302 removed outlier: 3.660A pdb=" N LEU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 333 removed outlier: 3.957A pdb=" N TYR B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Proline residue: B 321 - end of helix Processing helix chain 'C' and resid 14 through 20 removed outlier: 3.935A pdb=" N LEU C 19 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.550A pdb=" N GLU C 82 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 134 through 138 removed outlier: 4.636A pdb=" N ASN C 137 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 220 Processing helix chain 'C' and resid 220 through 233 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 241 through 261 removed outlier: 3.548A pdb=" N THR C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 302 removed outlier: 3.660A pdb=" N LEU C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 333 removed outlier: 3.956A pdb=" N TYR C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Proline residue: C 321 - end of helix Processing helix chain 'D' and resid 14 through 20 removed outlier: 3.934A pdb=" N LEU D 19 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.550A pdb=" N GLU D 82 " --> pdb=" O HIS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 134 through 138 removed outlier: 4.634A pdb=" N ASN D 137 " --> pdb=" O ASN D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 220 through 233 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 241 through 261 removed outlier: 3.548A pdb=" N THR D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 302 removed outlier: 3.660A pdb=" N LEU D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 333 removed outlier: 3.957A pdb=" N TYR D 318 " --> pdb=" O ARG D 314 " (cutoff:3.500A) Proline residue: D 321 - end of helix Processing helix chain 'E' and resid 14 through 20 removed outlier: 3.934A pdb=" N LEU E 19 " --> pdb=" O THR E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.549A pdb=" N GLU E 82 " --> pdb=" O HIS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 134 through 138 removed outlier: 4.634A pdb=" N ASN E 137 " --> pdb=" O ASN E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 220 through 233 Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 241 through 261 removed outlier: 3.547A pdb=" N THR E 247 " --> pdb=" O PRO E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 302 removed outlier: 3.661A pdb=" N LEU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 333 removed outlier: 3.957A pdb=" N TYR E 318 " --> pdb=" O ARG E 314 " (cutoff:3.500A) Proline residue: E 321 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 76 removed outlier: 6.187A pdb=" N THR A 106 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN A 126 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU A 108 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN A 53 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 40 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLN A 55 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP A 38 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLU A 57 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU A 36 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS A 59 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER A 34 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N PHE A 61 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ASP A 32 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP A 29 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ARG A 162 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 31 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 76 removed outlier: 6.187A pdb=" N THR A 106 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN A 126 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU A 108 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN A 53 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 40 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLN A 55 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP A 38 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLU A 57 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU A 36 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS A 59 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER A 34 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N PHE A 61 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ASP A 32 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.328A pdb=" N GLU A 148 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER A 201 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU A 198 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU A 192 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR A 200 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP A 190 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA A 202 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN A 188 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 204 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 186 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS A 206 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR A 184 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS A 208 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 74 through 76 removed outlier: 6.188A pdb=" N THR B 106 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN B 126 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU B 108 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 124 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN B 53 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE B 40 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLN B 55 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP B 38 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLU B 57 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU B 36 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS B 59 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER B 34 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N PHE B 61 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N ASP B 32 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP B 29 " --> pdb=" O GLN B 160 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ARG B 162 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B 31 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 76 removed outlier: 6.188A pdb=" N THR B 106 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN B 126 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU B 108 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 124 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN B 53 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE B 40 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLN B 55 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP B 38 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLU B 57 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU B 36 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS B 59 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER B 34 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N PHE B 61 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N ASP B 32 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 92 removed outlier: 4.328A pdb=" N GLU B 148 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER B 201 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU B 198 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 192 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR B 200 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP B 190 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA B 202 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN B 188 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE B 204 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 186 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS B 206 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR B 184 " --> pdb=" O HIS B 206 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HIS B 208 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 76 removed outlier: 6.187A pdb=" N THR C 106 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN C 126 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU C 108 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG C 124 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN C 53 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE C 40 " --> pdb=" O GLN C 53 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLN C 55 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP C 38 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLU C 57 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU C 36 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS C 59 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER C 34 " --> pdb=" O HIS C 59 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N PHE C 61 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N ASP C 32 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP C 29 " --> pdb=" O GLN C 160 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ARG C 162 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE C 31 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 74 through 76 removed outlier: 6.187A pdb=" N THR C 106 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN C 126 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU C 108 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG C 124 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN C 53 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE C 40 " --> pdb=" O GLN C 53 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLN C 55 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP C 38 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLU C 57 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU C 36 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS C 59 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER C 34 " --> pdb=" O HIS C 59 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N PHE C 61 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N ASP C 32 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 89 through 92 removed outlier: 4.327A pdb=" N GLU C 148 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER C 201 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU C 198 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU C 192 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR C 200 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP C 190 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA C 202 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN C 188 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE C 204 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL C 186 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS C 206 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR C 184 " --> pdb=" O HIS C 206 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N HIS C 208 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 74 through 76 removed outlier: 6.188A pdb=" N THR D 106 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN D 126 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU D 108 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG D 124 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN D 53 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE D 40 " --> pdb=" O GLN D 53 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLN D 55 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP D 38 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLU D 57 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU D 36 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS D 59 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER D 34 " --> pdb=" O HIS D 59 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N PHE D 61 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ASP D 32 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP D 29 " --> pdb=" O GLN D 160 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ARG D 162 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE D 31 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 74 through 76 removed outlier: 6.188A pdb=" N THR D 106 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN D 126 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU D 108 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG D 124 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN D 53 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE D 40 " --> pdb=" O GLN D 53 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLN D 55 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP D 38 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLU D 57 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU D 36 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS D 59 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER D 34 " --> pdb=" O HIS D 59 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N PHE D 61 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ASP D 32 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 89 through 92 removed outlier: 4.328A pdb=" N GLU D 148 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER D 201 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU D 198 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU D 192 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR D 200 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP D 190 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA D 202 " --> pdb=" O GLN D 188 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN D 188 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE D 204 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 186 " --> pdb=" O PHE D 204 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS D 206 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR D 184 " --> pdb=" O HIS D 206 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS D 208 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 74 through 76 removed outlier: 6.187A pdb=" N THR E 106 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN E 126 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU E 108 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG E 124 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS E 118 " --> pdb=" O ASP E 114 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN E 53 " --> pdb=" O PHE E 40 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE E 40 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLN E 55 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP E 38 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLU E 57 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU E 36 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS E 59 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER E 34 " --> pdb=" O HIS E 59 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N PHE E 61 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ASP E 32 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP E 29 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ARG E 162 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 31 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 74 through 76 removed outlier: 6.187A pdb=" N THR E 106 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN E 126 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU E 108 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG E 124 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS E 118 " --> pdb=" O ASP E 114 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN E 53 " --> pdb=" O PHE E 40 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE E 40 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLN E 55 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP E 38 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLU E 57 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU E 36 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS E 59 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER E 34 " --> pdb=" O HIS E 59 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N PHE E 61 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ASP E 32 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 89 through 92 removed outlier: 4.328A pdb=" N GLU E 148 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER E 201 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU E 198 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU E 192 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR E 200 " --> pdb=" O ASP E 190 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP E 190 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA E 202 " --> pdb=" O GLN E 188 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN E 188 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE E 204 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL E 186 " --> pdb=" O PHE E 204 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS E 206 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR E 184 " --> pdb=" O HIS E 206 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS E 208 " --> pdb=" O LYS E 182 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2010 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: 2.62 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2240 1.31 - 1.44: 4212 1.44 - 1.57: 8077 1.57 - 1.70: 3 1.70 - 1.83: 125 Bond restraints: 14657 Sorted by residual: bond pdb=" N LYS A 264 " pdb=" CA CLYS A 264 " ideal model delta sigma weight residual 1.455 1.584 -0.129 1.37e-02 5.33e+03 8.89e+01 bond pdb=" C37 IVM B 401 " pdb=" C38 IVM B 401 " ideal model delta sigma weight residual 1.450 1.327 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C37 IVM C 401 " pdb=" C38 IVM C 401 " ideal model delta sigma weight residual 1.450 1.327 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C37 IVM D 401 " pdb=" C38 IVM D 401 " ideal model delta sigma weight residual 1.450 1.327 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C37 IVM A 401 " pdb=" C38 IVM A 401 " ideal model delta sigma weight residual 1.450 1.328 0.122 2.00e-02 2.50e+03 3.74e+01 ... (remaining 14652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16118 1.99 - 3.98: 3165 3.98 - 5.97: 557 5.97 - 7.96: 91 7.96 - 9.95: 24 Bond angle restraints: 19955 Sorted by residual: angle pdb=" C CYS C 241 " pdb=" N ILE C 242 " pdb=" CA ILE C 242 " ideal model delta sigma weight residual 120.33 125.70 -5.37 8.00e-01 1.56e+00 4.50e+01 angle pdb=" C CYS D 241 " pdb=" N ILE D 242 " pdb=" CA ILE D 242 " ideal model delta sigma weight residual 120.33 125.69 -5.36 8.00e-01 1.56e+00 4.49e+01 angle pdb=" C CYS E 241 " pdb=" N ILE E 242 " pdb=" CA ILE E 242 " ideal model delta sigma weight residual 120.33 125.65 -5.32 8.00e-01 1.56e+00 4.41e+01 angle pdb=" N LYS A 264 " pdb=" CA CLYS A 264 " pdb=" C LYS A 264 " ideal model delta sigma weight residual 113.72 105.09 8.63 1.30e+00 5.92e-01 4.41e+01 angle pdb=" C CYS B 241 " pdb=" N ILE B 242 " pdb=" CA ILE B 242 " ideal model delta sigma weight residual 120.33 125.63 -5.30 8.00e-01 1.56e+00 4.38e+01 ... (remaining 19950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 8056 15.26 - 30.53: 872 30.53 - 45.79: 209 45.79 - 61.06: 61 61.06 - 76.32: 45 Dihedral angle restraints: 9243 sinusoidal: 4224 harmonic: 5019 Sorted by residual: dihedral pdb=" C ARG E 93 " pdb=" N ARG E 93 " pdb=" CA ARG E 93 " pdb=" CB ARG E 93 " ideal model delta harmonic sigma weight residual -122.60 -140.39 17.79 0 2.50e+00 1.60e-01 5.07e+01 dihedral pdb=" C ARG B 93 " pdb=" N ARG B 93 " pdb=" CA ARG B 93 " pdb=" CB ARG B 93 " ideal model delta harmonic sigma weight residual -122.60 -140.17 17.57 0 2.50e+00 1.60e-01 4.94e+01 dihedral pdb=" C ARG D 93 " pdb=" N ARG D 93 " pdb=" CA ARG D 93 " pdb=" CB ARG D 93 " ideal model delta harmonic sigma weight residual -122.60 -139.87 17.27 0 2.50e+00 1.60e-01 4.77e+01 ... (remaining 9240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1976 0.144 - 0.288: 263 0.288 - 0.432: 22 0.432 - 0.577: 5 0.577 - 0.721: 5 Chirality restraints: 2271 Sorted by residual: chirality pdb=" CA ARG E 93 " pdb=" N ARG E 93 " pdb=" C ARG E 93 " pdb=" CB ARG E 93 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA ARG B 93 " pdb=" N ARG B 93 " pdb=" C ARG B 93 " pdb=" CB ARG B 93 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CA ARG C 93 " pdb=" N ARG C 93 " pdb=" C ARG C 93 " pdb=" CB ARG C 93 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 2268 not shown) Planarity restraints: 2451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C37 IVM A 401 " -0.339 2.00e-02 2.50e+03 2.71e-01 9.21e+02 pdb=" C38 IVM A 401 " 0.457 2.00e-02 2.50e+03 pdb=" C39 IVM A 401 " 0.119 2.00e-02 2.50e+03 pdb=" C40 IVM A 401 " -0.150 2.00e-02 2.50e+03 pdb=" C47 IVM A 401 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM C 401 " -0.338 2.00e-02 2.50e+03 2.71e-01 9.15e+02 pdb=" C38 IVM C 401 " 0.457 2.00e-02 2.50e+03 pdb=" C39 IVM C 401 " 0.117 2.00e-02 2.50e+03 pdb=" C40 IVM C 401 " -0.146 2.00e-02 2.50e+03 pdb=" C47 IVM C 401 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM D 401 " -0.338 2.00e-02 2.50e+03 2.70e-01 9.14e+02 pdb=" C38 IVM D 401 " 0.455 2.00e-02 2.50e+03 pdb=" C39 IVM D 401 " 0.119 2.00e-02 2.50e+03 pdb=" C40 IVM D 401 " -0.152 2.00e-02 2.50e+03 pdb=" C47 IVM D 401 " -0.083 2.00e-02 2.50e+03 ... (remaining 2448 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 77 2.62 - 3.19: 12099 3.19 - 3.76: 21190 3.76 - 4.33: 31888 4.33 - 4.90: 52424 Nonbonded interactions: 117678 Sorted by model distance: nonbonded pdb=" NE ARG A 93 " pdb=" OD2 ASP E 38 " model vdw 2.051 3.120 nonbonded pdb=" OD2 ASP A 38 " pdb=" NE ARG B 93 " model vdw 2.052 3.120 nonbonded pdb=" OD2 ASP C 38 " pdb=" NE ARG D 93 " model vdw 2.053 3.120 nonbonded pdb=" OD2 ASP B 38 " pdb=" NE ARG C 93 " model vdw 2.053 3.120 nonbonded pdb=" OD2 ASP D 38 " pdb=" NE ARG E 93 " model vdw 2.054 3.120 ... (remaining 117673 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 263 or resid 265 through 333)) selection = (chain 'B' and (resid 3 through 263 or resid 265 through 333)) selection = (chain 'C' and (resid 3 through 263 or resid 265 through 333)) selection = (chain 'D' and (resid 3 through 263 or resid 265 through 333)) selection = (chain 'E' and (resid 3 through 263 or resid 265 through 333)) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.720 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.012 0.129 14667 Z= 0.728 Angle : 1.683 9.948 19975 Z= 1.071 Chirality : 0.107 0.721 2271 Planarity : 0.025 0.271 2451 Dihedral : 14.800 76.319 5941 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -0.84 (0.19), residues: 1651 helix: -1.50 (0.19), residues: 515 sheet: 1.36 (0.28), residues: 355 loop : -0.71 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.007 ARG C 122 TYR 0.031 0.009 TYR E 272 PHE 0.032 0.009 PHE D 100 TRP 0.042 0.012 TRP E 279 HIS 0.016 0.004 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.01186 (14657) covalent geometry : angle 1.68192 (19955) SS BOND : bond 0.07030 ( 10) SS BOND : angle 2.37486 ( 20) hydrogen bonds : bond 0.19475 ( 615) hydrogen bonds : angle 6.82053 ( 2010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.561 Fit side-chains REVERT: A 14 ASN cc_start: 0.4795 (t0) cc_final: 0.4535 (t0) REVERT: A 57 GLU cc_start: 0.8960 (tt0) cc_final: 0.8676 (tt0) REVERT: A 71 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6899 (mtp180) REVERT: A 101 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7342 (mt-10) REVERT: A 136 GLN cc_start: 0.7664 (tt0) cc_final: 0.6890 (mt0) REVERT: B 14 ASN cc_start: 0.4733 (t0) cc_final: 0.4488 (t0) REVERT: B 47 GLU cc_start: 0.7629 (mp0) cc_final: 0.7274 (mp0) REVERT: B 71 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6962 (mtp180) REVERT: B 101 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7261 (mt-10) REVERT: B 136 GLN cc_start: 0.7697 (tt0) cc_final: 0.6775 (mt0) REVERT: B 154 MET cc_start: 0.8376 (mtt) cc_final: 0.8143 (mtt) REVERT: C 14 ASN cc_start: 0.4692 (t0) cc_final: 0.4420 (t0) REVERT: C 57 GLU cc_start: 0.8989 (tt0) cc_final: 0.8785 (tt0) REVERT: C 71 ARG cc_start: 0.7127 (mtt-85) cc_final: 0.6754 (mtp180) REVERT: C 101 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7197 (mt-10) REVERT: C 162 ARG cc_start: 0.7242 (mtp180) cc_final: 0.7000 (mtm180) REVERT: D 14 ASN cc_start: 0.4811 (t0) cc_final: 0.4572 (t0) REVERT: D 71 ARG cc_start: 0.7279 (mtt-85) cc_final: 0.6980 (mtp180) REVERT: D 101 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7422 (mt-10) REVERT: D 294 TYR cc_start: 0.6612 (t80) cc_final: 0.6346 (t80) REVERT: E 14 ASN cc_start: 0.4718 (t0) cc_final: 0.4480 (t0) REVERT: E 71 ARG cc_start: 0.7339 (mtt-85) cc_final: 0.7035 (mmm160) REVERT: E 101 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7315 (mt-10) REVERT: E 136 GLN cc_start: 0.7783 (tt0) cc_final: 0.6808 (mt0) REVERT: E 176 MET cc_start: 0.7629 (mtp) cc_final: 0.7428 (mtp) REVERT: E 294 TYR cc_start: 0.6534 (t80) cc_final: 0.6263 (t80) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1464 time to fit residues: 53.4317 Evaluate side-chains 196 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 188 GLN B 188 GLN C 188 GLN D 188 GLN E 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105290 restraints weight = 41408.319| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.31 r_work: 0.2868 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14667 Z= 0.148 Angle : 0.675 6.469 19975 Z= 0.350 Chirality : 0.047 0.190 2271 Planarity : 0.004 0.029 2451 Dihedral : 10.136 74.483 2537 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.66 % Allowed : 8.37 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.82 (0.21), residues: 1651 helix: 0.87 (0.23), residues: 510 sheet: 1.19 (0.27), residues: 405 loop : 0.05 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 74 TYR 0.011 0.001 TYR C 294 PHE 0.011 0.001 PHE A 174 TRP 0.021 0.002 TRP A 232 HIS 0.004 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00341 (14657) covalent geometry : angle 0.66979 (19955) SS BOND : bond 0.00340 ( 10) SS BOND : angle 2.71663 ( 20) hydrogen bonds : bond 0.04773 ( 615) hydrogen bonds : angle 4.14297 ( 2010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.445 Fit side-chains REVERT: A 39 ARG cc_start: 0.7528 (mtt90) cc_final: 0.6758 (ttt-90) REVERT: A 57 GLU cc_start: 0.9079 (tt0) cc_final: 0.8826 (tt0) REVERT: A 88 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8146 (t70) REVERT: A 101 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7467 (mt-10) REVERT: A 136 GLN cc_start: 0.8674 (tt0) cc_final: 0.7842 (mt0) REVERT: A 189 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7373 (tttp) REVERT: B 39 ARG cc_start: 0.7475 (mtt90) cc_final: 0.6637 (ttt-90) REVERT: B 47 GLU cc_start: 0.8640 (mp0) cc_final: 0.8199 (mp0) REVERT: B 101 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7396 (mt-10) REVERT: B 136 GLN cc_start: 0.8609 (tt0) cc_final: 0.7791 (mt0) REVERT: B 189 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7273 (tttp) REVERT: B 332 TRP cc_start: 0.8528 (m100) cc_final: 0.8196 (m100) REVERT: C 39 ARG cc_start: 0.7622 (mtt90) cc_final: 0.6784 (ttp80) REVERT: C 101 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7391 (mt-10) REVERT: C 136 GLN cc_start: 0.8622 (tt0) cc_final: 0.7805 (mt0) REVERT: C 265 GLN cc_start: 0.8125 (mm110) cc_final: 0.7876 (mm-40) REVERT: D 39 ARG cc_start: 0.7624 (mtt90) cc_final: 0.6760 (ttt-90) REVERT: D 101 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7407 (mt-10) REVERT: D 107 ARG cc_start: 0.8621 (mmt180) cc_final: 0.8408 (mmt180) REVERT: D 136 GLN cc_start: 0.8558 (tt0) cc_final: 0.7763 (mt0) REVERT: D 265 GLN cc_start: 0.8325 (mm110) cc_final: 0.7989 (mm-40) REVERT: E 39 ARG cc_start: 0.7535 (mtt90) cc_final: 0.6671 (ttt-90) REVERT: E 101 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7556 (mt-10) REVERT: E 120 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8046 (ttt-90) REVERT: E 136 GLN cc_start: 0.8670 (tt0) cc_final: 0.7826 (mt0) outliers start: 26 outliers final: 14 residues processed: 254 average time/residue: 0.1333 time to fit residues: 48.8140 Evaluate side-chains 211 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 73 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 59 HIS B 187 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.122486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.097832 restraints weight = 57102.855| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.88 r_work: 0.2720 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14667 Z= 0.133 Angle : 0.591 6.387 19975 Z= 0.303 Chirality : 0.045 0.151 2271 Planarity : 0.004 0.032 2451 Dihedral : 9.297 75.280 2537 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.02 % Allowed : 11.75 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.16 (0.22), residues: 1651 helix: 1.42 (0.23), residues: 510 sheet: 1.26 (0.27), residues: 415 loop : 0.10 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 74 TYR 0.013 0.001 TYR E 43 PHE 0.009 0.001 PHE B 174 TRP 0.011 0.001 TRP B 60 HIS 0.004 0.001 HIS E 44 Details of bonding type rmsd covalent geometry : bond 0.00312 (14657) covalent geometry : angle 0.58757 (19955) SS BOND : bond 0.00159 ( 10) SS BOND : angle 2.18234 ( 20) hydrogen bonds : bond 0.04003 ( 615) hydrogen bonds : angle 3.86832 ( 2010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.570 Fit side-chains REVERT: A 47 GLU cc_start: 0.8601 (mp0) cc_final: 0.7811 (mp0) REVERT: A 57 GLU cc_start: 0.9077 (tt0) cc_final: 0.8838 (tt0) REVERT: A 70 ASP cc_start: 0.7723 (m-30) cc_final: 0.7360 (p0) REVERT: A 88 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8104 (t70) REVERT: A 101 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7257 (mt-10) REVERT: A 136 GLN cc_start: 0.8689 (tt0) cc_final: 0.7960 (mt0) REVERT: A 189 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7477 (tttp) REVERT: B 47 GLU cc_start: 0.8695 (mp0) cc_final: 0.8355 (mp0) REVERT: B 101 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7337 (mt-10) REVERT: B 107 ARG cc_start: 0.8507 (mmt180) cc_final: 0.8262 (mmt180) REVERT: B 136 GLN cc_start: 0.8551 (tt0) cc_final: 0.7768 (mt0) REVERT: B 189 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7346 (tttp) REVERT: B 265 GLN cc_start: 0.8134 (mm110) cc_final: 0.7914 (mm-40) REVERT: C 39 ARG cc_start: 0.7601 (mtt90) cc_final: 0.6718 (ttt90) REVERT: C 57 GLU cc_start: 0.9110 (tt0) cc_final: 0.8873 (tt0) REVERT: C 101 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7331 (mt-10) REVERT: C 136 GLN cc_start: 0.8593 (tt0) cc_final: 0.7785 (mt0) REVERT: C 189 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7350 (tttp) REVERT: D 70 ASP cc_start: 0.7899 (m-30) cc_final: 0.7681 (p0) REVERT: D 101 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7393 (mt-10) REVERT: D 107 ARG cc_start: 0.8546 (mmt180) cc_final: 0.8310 (mmt180) REVERT: D 136 GLN cc_start: 0.8545 (tt0) cc_final: 0.7781 (mt0) REVERT: E 101 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7455 (mt-10) REVERT: E 120 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8144 (ttt-90) REVERT: E 136 GLN cc_start: 0.8666 (tt0) cc_final: 0.7897 (mt0) REVERT: E 189 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7282 (tttp) REVERT: E 236 TRP cc_start: 0.8353 (m-90) cc_final: 0.7882 (m100) REVERT: E 265 GLN cc_start: 0.8223 (mm110) cc_final: 0.8004 (mm-40) outliers start: 16 outliers final: 13 residues processed: 256 average time/residue: 0.1536 time to fit residues: 54.3781 Evaluate side-chains 226 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 23 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 187 HIS B 157 ASN C 157 ASN C 187 HIS D 59 HIS D 187 HIS E 187 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.093100 restraints weight = 42802.424| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.12 r_work: 0.2709 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14667 Z= 0.191 Angle : 0.629 6.701 19975 Z= 0.320 Chirality : 0.047 0.153 2271 Planarity : 0.004 0.033 2451 Dihedral : 9.221 75.709 2537 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.43 % Allowed : 12.39 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.00 (0.21), residues: 1651 helix: 1.43 (0.22), residues: 510 sheet: 1.25 (0.27), residues: 405 loop : -0.16 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 74 TYR 0.015 0.001 TYR E 43 PHE 0.010 0.001 PHE D 123 TRP 0.009 0.001 TRP A 60 HIS 0.004 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00473 (14657) covalent geometry : angle 0.62473 (19955) SS BOND : bond 0.00175 ( 10) SS BOND : angle 2.26513 ( 20) hydrogen bonds : bond 0.04174 ( 615) hydrogen bonds : angle 3.90610 ( 2010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.471 Fit side-chains REVERT: A 57 GLU cc_start: 0.9021 (tt0) cc_final: 0.8813 (tt0) REVERT: A 88 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8077 (t70) REVERT: A 101 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7253 (mt-10) REVERT: A 122 ARG cc_start: 0.8930 (ttm-80) cc_final: 0.8683 (ttp-170) REVERT: A 136 GLN cc_start: 0.8736 (tt0) cc_final: 0.8073 (mt0) REVERT: A 189 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7608 (tttp) REVERT: B 47 GLU cc_start: 0.8805 (mp0) cc_final: 0.8461 (mp0) REVERT: B 101 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7345 (mt-10) REVERT: B 107 ARG cc_start: 0.8559 (mmt180) cc_final: 0.8320 (mmt180) REVERT: B 136 GLN cc_start: 0.8537 (tt0) cc_final: 0.7859 (mt0) REVERT: B 189 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7524 (tttp) REVERT: B 265 GLN cc_start: 0.8273 (mm110) cc_final: 0.8057 (mm-40) REVERT: C 57 GLU cc_start: 0.9095 (tt0) cc_final: 0.8861 (tt0) REVERT: C 101 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7353 (mt-10) REVERT: C 136 GLN cc_start: 0.8566 (tt0) cc_final: 0.7840 (mt0) REVERT: C 189 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7544 (tttp) REVERT: C 197 ASN cc_start: 0.8589 (m110) cc_final: 0.8305 (m110) REVERT: C 319 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7843 (mm) REVERT: D 101 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7431 (mt-10) REVERT: D 107 ARG cc_start: 0.8592 (mmt180) cc_final: 0.8354 (mmt180) REVERT: D 136 GLN cc_start: 0.8541 (tt0) cc_final: 0.7845 (mt0) REVERT: D 189 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7496 (tttp) REVERT: E 101 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7483 (mt-10) REVERT: E 120 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8287 (ttp-170) REVERT: E 136 GLN cc_start: 0.8661 (tt0) cc_final: 0.7978 (mt0) REVERT: E 189 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7441 (tttp) REVERT: E 236 TRP cc_start: 0.8414 (m-90) cc_final: 0.8007 (m100) REVERT: E 265 GLN cc_start: 0.8278 (mm110) cc_final: 0.8054 (mm-40) outliers start: 38 outliers final: 28 residues processed: 240 average time/residue: 0.1482 time to fit residues: 49.0706 Evaluate side-chains 247 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 157 ASN C 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.122371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.097739 restraints weight = 48567.176| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.17 r_work: 0.2784 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14667 Z= 0.135 Angle : 0.565 5.965 19975 Z= 0.288 Chirality : 0.045 0.150 2271 Planarity : 0.004 0.032 2451 Dihedral : 8.987 77.384 2537 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.36 % Allowed : 12.96 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.11 (0.21), residues: 1651 helix: 1.62 (0.22), residues: 510 sheet: 1.30 (0.27), residues: 405 loop : -0.16 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 74 TYR 0.014 0.001 TYR E 43 PHE 0.008 0.001 PHE D 123 TRP 0.010 0.001 TRP B 60 HIS 0.003 0.001 HIS E 44 Details of bonding type rmsd covalent geometry : bond 0.00325 (14657) covalent geometry : angle 0.56199 (19955) SS BOND : bond 0.00283 ( 10) SS BOND : angle 1.89408 ( 20) hydrogen bonds : bond 0.03687 ( 615) hydrogen bonds : angle 3.80477 ( 2010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8971 (tt0) cc_final: 0.8755 (tt0) REVERT: A 88 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8104 (t70) REVERT: A 101 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7181 (mt-10) REVERT: A 134 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7638 (t0) REVERT: A 189 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7631 (tttp) REVERT: B 47 GLU cc_start: 0.8772 (mp0) cc_final: 0.8503 (mp0) REVERT: B 101 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7258 (mt-10) REVERT: B 107 ARG cc_start: 0.8547 (mmt180) cc_final: 0.8283 (mmt180) REVERT: B 120 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8259 (ttt-90) REVERT: B 136 GLN cc_start: 0.8511 (tt0) cc_final: 0.7905 (mt0) REVERT: B 162 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7936 (mtm180) REVERT: B 189 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7512 (tttp) REVERT: B 293 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7758 (tp30) REVERT: C 57 GLU cc_start: 0.9056 (tt0) cc_final: 0.8828 (tt0) REVERT: C 101 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7273 (mt-10) REVERT: C 136 GLN cc_start: 0.8544 (tt0) cc_final: 0.7902 (mt0) REVERT: C 189 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7565 (tttp) REVERT: C 197 ASN cc_start: 0.8556 (m110) cc_final: 0.8255 (m110) REVERT: C 218 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8100 (mp) REVERT: C 319 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7793 (mm) REVERT: D 101 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7366 (mt-10) REVERT: D 107 ARG cc_start: 0.8574 (mmt180) cc_final: 0.8340 (mmt180) REVERT: D 120 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8250 (ttt-90) REVERT: D 136 GLN cc_start: 0.8507 (tt0) cc_final: 0.7857 (mt0) REVERT: D 189 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7577 (tttp) REVERT: E 101 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7389 (mt-10) REVERT: E 120 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8276 (ttt180) REVERT: E 122 ARG cc_start: 0.8796 (ttm170) cc_final: 0.8555 (ttm170) REVERT: E 134 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7567 (t0) REVERT: E 136 GLN cc_start: 0.8633 (tt0) cc_final: 0.7980 (mt0) REVERT: E 189 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7501 (tttp) REVERT: E 218 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8260 (mt) REVERT: E 236 TRP cc_start: 0.8444 (m-90) cc_final: 0.8005 (m100) outliers start: 37 outliers final: 26 residues processed: 253 average time/residue: 0.1629 time to fit residues: 55.9321 Evaluate side-chains 251 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 40 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 100 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 157 ASN C 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103153 restraints weight = 36648.928| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.93 r_work: 0.2919 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14667 Z= 0.128 Angle : 0.552 5.929 19975 Z= 0.282 Chirality : 0.045 0.150 2271 Planarity : 0.004 0.031 2451 Dihedral : 8.850 78.789 2537 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.55 % Allowed : 13.15 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.18 (0.21), residues: 1651 helix: 1.74 (0.22), residues: 510 sheet: 1.24 (0.27), residues: 415 loop : -0.14 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.014 0.001 TYR E 43 PHE 0.007 0.001 PHE E 123 TRP 0.009 0.001 TRP B 60 HIS 0.003 0.001 HIS E 44 Details of bonding type rmsd covalent geometry : bond 0.00308 (14657) covalent geometry : angle 0.54929 (19955) SS BOND : bond 0.00185 ( 10) SS BOND : angle 1.76555 ( 20) hydrogen bonds : bond 0.03554 ( 615) hydrogen bonds : angle 3.77433 ( 2010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8295 (ttm170) cc_final: 0.8092 (ttm170) REVERT: A 101 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6819 (mt-10) REVERT: A 134 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7413 (t0) REVERT: A 189 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7274 (tttp) REVERT: B 47 GLU cc_start: 0.8659 (mp0) cc_final: 0.8351 (mp0) REVERT: B 101 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6954 (mt-10) REVERT: B 107 ARG cc_start: 0.8372 (mmt180) cc_final: 0.8061 (mmt180) REVERT: B 120 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8038 (ttt-90) REVERT: B 136 GLN cc_start: 0.8324 (tt0) cc_final: 0.7604 (mt0) REVERT: B 189 LYS cc_start: 0.7959 (ttpt) cc_final: 0.7260 (tttp) REVERT: B 293 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7485 (tp30) REVERT: C 57 GLU cc_start: 0.9077 (tt0) cc_final: 0.8836 (tt0) REVERT: C 101 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7040 (mt-10) REVERT: C 136 GLN cc_start: 0.8391 (tt0) cc_final: 0.7553 (mp10) REVERT: C 189 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7195 (tttp) REVERT: C 197 ASN cc_start: 0.8486 (m110) cc_final: 0.8186 (m110) REVERT: C 218 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7866 (mp) REVERT: C 319 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7409 (mm) REVERT: D 101 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7020 (mt-10) REVERT: D 107 ARG cc_start: 0.8425 (mmt180) cc_final: 0.8154 (mmt180) REVERT: D 120 ARG cc_start: 0.8508 (ttp80) cc_final: 0.7989 (ttt-90) REVERT: D 136 GLN cc_start: 0.8401 (tt0) cc_final: 0.7525 (mp10) REVERT: D 180 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8059 (mt) REVERT: D 189 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7271 (tttp) REVERT: E 101 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7085 (mt-10) REVERT: E 120 ARG cc_start: 0.8424 (ttp80) cc_final: 0.7947 (ttt-90) REVERT: E 134 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7445 (t0) REVERT: E 136 GLN cc_start: 0.8503 (tt0) cc_final: 0.7788 (mt0) REVERT: E 189 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7249 (tttp) REVERT: E 218 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7937 (mp) REVERT: E 236 TRP cc_start: 0.8212 (m-90) cc_final: 0.7777 (m100) REVERT: E 315 LYS cc_start: 0.6997 (mttt) cc_final: 0.6645 (mtmt) outliers start: 40 outliers final: 27 residues processed: 246 average time/residue: 0.1579 time to fit residues: 53.2235 Evaluate side-chains 246 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 124 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN B 157 ASN C 157 ASN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.100994 restraints weight = 52878.938| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.74 r_work: 0.2798 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14667 Z= 0.187 Angle : 0.607 6.308 19975 Z= 0.308 Chirality : 0.046 0.155 2271 Planarity : 0.004 0.031 2451 Dihedral : 8.946 78.415 2537 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.94 % Allowed : 12.90 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.99 (0.21), residues: 1651 helix: 1.64 (0.22), residues: 510 sheet: 1.24 (0.27), residues: 405 loop : -0.36 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 74 TYR 0.016 0.001 TYR E 43 PHE 0.010 0.001 PHE D 123 TRP 0.008 0.001 TRP A 60 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00465 (14657) covalent geometry : angle 0.60340 (19955) SS BOND : bond 0.00240 ( 10) SS BOND : angle 2.20953 ( 20) hydrogen bonds : bond 0.03947 ( 615) hydrogen bonds : angle 3.87717 ( 2010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8087 (t70) REVERT: A 101 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6932 (mt-10) REVERT: A 120 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8227 (ttp-170) REVERT: A 134 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7472 (t0) REVERT: A 189 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7293 (tttp) REVERT: B 47 GLU cc_start: 0.8702 (mp0) cc_final: 0.8323 (mp0) REVERT: B 101 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7004 (mt-10) REVERT: B 107 ARG cc_start: 0.8421 (mmt180) cc_final: 0.8121 (mmt180) REVERT: B 120 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8130 (ttt-90) REVERT: B 136 GLN cc_start: 0.8393 (tt0) cc_final: 0.7644 (mt0) REVERT: B 189 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7258 (tttp) REVERT: C 57 GLU cc_start: 0.9163 (tt0) cc_final: 0.8937 (tt0) REVERT: C 101 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7060 (mt-10) REVERT: C 136 GLN cc_start: 0.8455 (tt0) cc_final: 0.7573 (mp10) REVERT: C 189 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7215 (tttp) REVERT: C 218 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7886 (mp) REVERT: C 319 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7363 (mm) REVERT: D 101 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7048 (mt-10) REVERT: D 107 ARG cc_start: 0.8488 (mmt180) cc_final: 0.8216 (mmt180) REVERT: D 120 ARG cc_start: 0.8677 (ttp80) cc_final: 0.8114 (ttt-90) REVERT: D 136 GLN cc_start: 0.8410 (tt0) cc_final: 0.7700 (mt0) REVERT: D 154 MET cc_start: 0.8873 (mtt) cc_final: 0.8549 (mtt) REVERT: D 189 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7281 (tttp) REVERT: E 101 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7157 (mt-10) REVERT: E 120 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8147 (ttp-170) REVERT: E 134 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7320 (t0) REVERT: E 136 GLN cc_start: 0.8531 (tt0) cc_final: 0.7706 (mt0) REVERT: E 189 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7227 (tttp) REVERT: E 218 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8027 (mt) REVERT: E 236 TRP cc_start: 0.8226 (m-90) cc_final: 0.7829 (m100) REVERT: E 315 LYS cc_start: 0.6968 (mttt) cc_final: 0.6623 (mtmt) outliers start: 46 outliers final: 40 residues processed: 233 average time/residue: 0.1556 time to fit residues: 49.9101 Evaluate side-chains 250 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 77 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN C 157 ASN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.100367 restraints weight = 39332.079| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.12 r_work: 0.2826 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14667 Z= 0.171 Angle : 0.594 6.474 19975 Z= 0.301 Chirality : 0.046 0.155 2271 Planarity : 0.004 0.031 2451 Dihedral : 8.929 78.641 2537 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.75 % Allowed : 12.96 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.95 (0.21), residues: 1651 helix: 1.72 (0.22), residues: 505 sheet: 1.20 (0.27), residues: 405 loop : -0.45 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.015 0.001 TYR E 43 PHE 0.009 0.001 PHE D 123 TRP 0.009 0.001 TRP A 60 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00423 (14657) covalent geometry : angle 0.59058 (19955) SS BOND : bond 0.00282 ( 10) SS BOND : angle 2.09345 ( 20) hydrogen bonds : bond 0.03864 ( 615) hydrogen bonds : angle 3.87581 ( 2010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8132 (t70) REVERT: A 101 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7056 (mt-10) REVERT: A 120 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8313 (ttp-170) REVERT: A 134 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7662 (t0) REVERT: A 189 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7526 (tttp) REVERT: B 47 GLU cc_start: 0.8777 (mp0) cc_final: 0.8421 (mp0) REVERT: B 101 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7153 (mt-10) REVERT: B 107 ARG cc_start: 0.8477 (mmt180) cc_final: 0.8192 (mmt180) REVERT: B 120 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8208 (ttt-90) REVERT: B 136 GLN cc_start: 0.8461 (tt0) cc_final: 0.7805 (mt0) REVERT: B 189 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7424 (tttp) REVERT: C 57 GLU cc_start: 0.9089 (tt0) cc_final: 0.8864 (tt0) REVERT: C 101 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7219 (mt-10) REVERT: C 136 GLN cc_start: 0.8502 (tt0) cc_final: 0.7732 (mp10) REVERT: C 189 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7463 (tttp) REVERT: C 218 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8021 (mp) REVERT: C 319 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7643 (mm) REVERT: D 101 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7194 (mt-10) REVERT: D 107 ARG cc_start: 0.8547 (mmt180) cc_final: 0.8293 (mmt180) REVERT: D 120 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8181 (ttt-90) REVERT: D 136 GLN cc_start: 0.8470 (tt0) cc_final: 0.7833 (mt0) REVERT: D 154 MET cc_start: 0.8949 (mtt) cc_final: 0.8644 (mtt) REVERT: D 189 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7437 (tttp) REVERT: E 101 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7288 (mt-10) REVERT: E 120 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8227 (ttp-170) REVERT: E 134 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7486 (t0) REVERT: E 136 GLN cc_start: 0.8591 (tt0) cc_final: 0.7866 (mt0) REVERT: E 189 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7404 (tttp) REVERT: E 218 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8117 (mp) REVERT: E 315 LYS cc_start: 0.7237 (mttt) cc_final: 0.6880 (mtmt) outliers start: 43 outliers final: 37 residues processed: 222 average time/residue: 0.1575 time to fit residues: 48.1822 Evaluate side-chains 238 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 163 optimal weight: 0.0970 chunk 66 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 82 optimal weight: 0.0040 chunk 145 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 157 ASN C 157 ASN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105642 restraints weight = 53583.376| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.74 r_work: 0.2861 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14667 Z= 0.107 Angle : 0.529 8.568 19975 Z= 0.270 Chirality : 0.044 0.151 2271 Planarity : 0.003 0.030 2451 Dihedral : 8.701 80.592 2537 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.72 % Allowed : 13.92 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.21 (0.21), residues: 1651 helix: 1.90 (0.22), residues: 505 sheet: 1.29 (0.27), residues: 415 loop : -0.24 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.013 0.001 TYR C 294 PHE 0.007 0.001 PHE C 123 TRP 0.011 0.001 TRP B 60 HIS 0.003 0.001 HIS E 44 Details of bonding type rmsd covalent geometry : bond 0.00247 (14657) covalent geometry : angle 0.52633 (19955) SS BOND : bond 0.00221 ( 10) SS BOND : angle 1.65170 ( 20) hydrogen bonds : bond 0.03260 ( 615) hydrogen bonds : angle 3.74276 ( 2010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6719 (mt-10) REVERT: A 120 ARG cc_start: 0.8487 (ttp80) cc_final: 0.7946 (ttp-170) REVERT: A 134 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7470 (t0) REVERT: A 189 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7263 (tttp) REVERT: B 47 GLU cc_start: 0.8646 (mp0) cc_final: 0.8382 (mp0) REVERT: B 101 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6909 (mt-10) REVERT: B 107 ARG cc_start: 0.8439 (mmt180) cc_final: 0.8127 (mmt180) REVERT: B 120 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8081 (ttt-90) REVERT: B 136 GLN cc_start: 0.8360 (tt0) cc_final: 0.7670 (mt0) REVERT: B 189 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7201 (tttp) REVERT: C 57 GLU cc_start: 0.9097 (tt0) cc_final: 0.8881 (tt0) REVERT: C 101 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6877 (mt-10) REVERT: C 136 GLN cc_start: 0.8409 (tt0) cc_final: 0.7668 (mt0) REVERT: C 169 MET cc_start: 0.7681 (ttt) cc_final: 0.7222 (ttt) REVERT: C 189 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7238 (tttp) REVERT: C 218 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7890 (mp) REVERT: C 319 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7257 (mm) REVERT: C 326 LEU cc_start: 0.7801 (tp) cc_final: 0.7435 (mp) REVERT: D 10 ILE cc_start: 0.8525 (mt) cc_final: 0.8306 (tp) REVERT: D 101 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6906 (mt-10) REVERT: D 107 ARG cc_start: 0.8459 (mmt180) cc_final: 0.8221 (mmt180) REVERT: D 120 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8040 (ttt-90) REVERT: D 136 GLN cc_start: 0.8409 (tt0) cc_final: 0.7578 (mp10) REVERT: D 189 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7239 (tttp) REVERT: E 101 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6906 (mt-10) REVERT: E 120 ARG cc_start: 0.8490 (ttp80) cc_final: 0.7915 (ttt-90) REVERT: E 134 ASN cc_start: 0.7880 (p0) cc_final: 0.7453 (t0) REVERT: E 136 GLN cc_start: 0.8559 (tt0) cc_final: 0.7875 (mt0) REVERT: E 189 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7166 (tttp) REVERT: E 315 LYS cc_start: 0.6875 (mttt) cc_final: 0.6279 (mtmt) REVERT: E 319 LEU cc_start: 0.7565 (mt) cc_final: 0.7354 (mm) outliers start: 27 outliers final: 19 residues processed: 233 average time/residue: 0.1633 time to fit residues: 51.7835 Evaluate side-chains 226 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN C 157 ASN E 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.122691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.098364 restraints weight = 50819.030| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.52 r_work: 0.2790 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14667 Z= 0.126 Angle : 0.558 7.883 19975 Z= 0.283 Chirality : 0.044 0.152 2271 Planarity : 0.004 0.032 2451 Dihedral : 8.693 80.890 2537 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.72 % Allowed : 14.11 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.20 (0.21), residues: 1651 helix: 1.89 (0.22), residues: 505 sheet: 1.30 (0.27), residues: 415 loop : -0.26 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 74 TYR 0.012 0.001 TYR E 43 PHE 0.008 0.001 PHE E 123 TRP 0.010 0.001 TRP A 60 HIS 0.003 0.001 HIS E 44 Details of bonding type rmsd covalent geometry : bond 0.00303 (14657) covalent geometry : angle 0.55477 (19955) SS BOND : bond 0.00238 ( 10) SS BOND : angle 1.86825 ( 20) hydrogen bonds : bond 0.03409 ( 615) hydrogen bonds : angle 3.76121 ( 2010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7083 (mt-10) REVERT: A 107 ARG cc_start: 0.8531 (mmt180) cc_final: 0.8251 (mmt180) REVERT: A 120 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8200 (ttp-170) REVERT: A 134 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7780 (t0) REVERT: A 162 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7930 (mtm180) REVERT: A 189 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7621 (tttp) REVERT: A 315 LYS cc_start: 0.7233 (mttt) cc_final: 0.6867 (mtpt) REVERT: B 47 GLU cc_start: 0.8828 (mp0) cc_final: 0.8603 (mp0) REVERT: B 101 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7208 (mt-10) REVERT: B 107 ARG cc_start: 0.8508 (mmt180) cc_final: 0.8217 (mmt180) REVERT: B 120 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8277 (ttt-90) REVERT: B 136 GLN cc_start: 0.8515 (tt0) cc_final: 0.7973 (mt0) REVERT: B 189 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7580 (tttp) REVERT: C 101 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7241 (mt-10) REVERT: C 136 GLN cc_start: 0.8533 (tt0) cc_final: 0.7936 (mt0) REVERT: C 189 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7621 (tttp) REVERT: C 218 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8171 (mp) REVERT: C 236 TRP cc_start: 0.8397 (m-90) cc_final: 0.8123 (m100) REVERT: C 319 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7729 (mm) REVERT: D 101 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7216 (mt-10) REVERT: D 107 ARG cc_start: 0.8528 (mmt180) cc_final: 0.8305 (mmt180) REVERT: D 136 GLN cc_start: 0.8506 (tt0) cc_final: 0.7868 (mp10) REVERT: D 189 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7622 (tttp) REVERT: E 101 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7236 (mt-10) REVERT: E 120 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8257 (ttt-90) REVERT: E 134 ASN cc_start: 0.8112 (p0) cc_final: 0.7773 (t0) REVERT: E 136 GLN cc_start: 0.8652 (tt0) cc_final: 0.8112 (mt0) REVERT: E 189 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7518 (tttp) REVERT: E 315 LYS cc_start: 0.7349 (mttt) cc_final: 0.6989 (mtmt) outliers start: 27 outliers final: 22 residues processed: 223 average time/residue: 0.1681 time to fit residues: 51.1690 Evaluate side-chains 224 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 1 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN C 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.123666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.097864 restraints weight = 40717.127| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.99 r_work: 0.2798 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14667 Z= 0.113 Angle : 0.551 7.867 19975 Z= 0.279 Chirality : 0.044 0.151 2271 Planarity : 0.003 0.031 2451 Dihedral : 8.670 81.606 2537 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.85 % Allowed : 13.92 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.23 (0.22), residues: 1651 helix: 1.93 (0.22), residues: 505 sheet: 1.29 (0.27), residues: 415 loop : -0.23 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.013 0.001 TYR E 43 PHE 0.007 0.001 PHE D 123 TRP 0.011 0.001 TRP A 60 HIS 0.003 0.001 HIS E 44 Details of bonding type rmsd covalent geometry : bond 0.00267 (14657) covalent geometry : angle 0.54852 (19955) SS BOND : bond 0.00245 ( 10) SS BOND : angle 1.81627 ( 20) hydrogen bonds : bond 0.03303 ( 615) hydrogen bonds : angle 3.73759 ( 2010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3492.05 seconds wall clock time: 60 minutes 32.99 seconds (3632.99 seconds total)