Starting phenix.real_space_refine on Fri Jul 3 11:54:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l6q_23207/07_2026/7l6q_23207.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l6q_23207/07_2026/7l6q_23207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l6q_23207/07_2026/7l6q_23207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l6q_23207/07_2026/7l6q_23207.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l6q_23207/07_2026/7l6q_23207.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l6q_23207/07_2026/7l6q_23207.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l6q_23207/07_2026/7l6q_23207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l6q_23207/07_2026/7l6q_23207.cif" } resolution = 2.5 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= 0.013 sd= 0.225 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 30 5.16 5 C 8760 2.51 5 N 2115 2.21 5 O 2410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13330 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "D" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "E" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 182 Unusual residues: {'CDL': 1, 'PGW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 131 Unusual residues: {'CDL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 131 Unusual residues: {'CDL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 131 Unusual residues: {'CDL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 80 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Time building chain proxies: 3.13, per 1000 atoms: 0.23 Number of scatterers: 13330 At special positions: 0 Unit cell: (90.132, 90.132, 120.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 15 15.00 O 2410 8.00 N 2115 7.00 C 8760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 580.8 milliseconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 40.8% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 removed outlier: 4.064A pdb=" N LYS A 54 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 removed outlier: 4.113A pdb=" N ARG A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.615A pdb=" N ILE A 157 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.558A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.730A pdb=" N LEU A 225 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 251 removed outlier: 3.646A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 286 Processing helix chain 'A' and resid 294 through 321 removed outlier: 4.389A pdb=" N GLN A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.997A pdb=" N ILE A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 4.064A pdb=" N LYS B 54 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 69 removed outlier: 4.113A pdb=" N ARG B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.615A pdb=" N ILE B 157 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.558A pdb=" N LEU B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.730A pdb=" N LEU B 225 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 251 removed outlier: 3.645A pdb=" N PHE B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 286 Processing helix chain 'B' and resid 294 through 321 removed outlier: 4.389A pdb=" N GLN B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.997A pdb=" N ILE B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 4.063A pdb=" N LYS C 54 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 removed outlier: 4.113A pdb=" N ARG C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.615A pdb=" N ILE C 157 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.558A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.730A pdb=" N LEU C 225 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 251 removed outlier: 3.646A pdb=" N PHE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 286 Processing helix chain 'C' and resid 294 through 321 removed outlier: 4.389A pdb=" N GLN C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C 302 " --> pdb=" O GLN C 298 " (cutoff:3.500A) Proline residue: C 305 - end of helix removed outlier: 3.997A pdb=" N ILE C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 4.064A pdb=" N LYS D 54 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 removed outlier: 3.591A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.615A pdb=" N ILE D 157 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.558A pdb=" N LEU D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 225 removed outlier: 3.729A pdb=" N LEU D 225 " --> pdb=" O VAL D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 251 removed outlier: 3.645A pdb=" N PHE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 286 Processing helix chain 'D' and resid 294 through 321 removed outlier: 4.388A pdb=" N GLN D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) Proline residue: D 305 - end of helix removed outlier: 3.997A pdb=" N ILE D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 4.064A pdb=" N LYS E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 69 removed outlier: 4.113A pdb=" N ARG E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 154 through 158 removed outlier: 3.614A pdb=" N ILE E 157 " --> pdb=" O ASN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.558A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 225 removed outlier: 3.730A pdb=" N LEU E 225 " --> pdb=" O VAL E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 251 removed outlier: 3.647A pdb=" N PHE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR E 237 " --> pdb=" O GLN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 286 Processing helix chain 'E' and resid 294 through 321 removed outlier: 4.389A pdb=" N GLN E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) Proline residue: E 305 - end of helix removed outlier: 3.998A pdb=" N ILE E 320 " --> pdb=" O VAL E 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 6.360A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 14 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A 142 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 20 " --> pdb=" O GLN A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.682A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP A 196 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LYS A 165 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 198 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG A 163 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.360A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL B 14 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE B 142 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 20 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.682A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 196 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LYS B 165 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 198 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG B 163 " --> pdb=" O VAL B 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 59 removed outlier: 6.361A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 14 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE C 142 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 20 " --> pdb=" O GLN C 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.682A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP C 196 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LYS C 165 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL C 198 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG C 163 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 56 through 59 removed outlier: 6.360A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL D 14 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE D 142 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 20 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.683A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP D 196 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LYS D 165 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL D 198 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG D 163 " --> pdb=" O VAL D 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 56 through 59 removed outlier: 6.360A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL E 14 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE E 142 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 20 " --> pdb=" O GLN E 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.682A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP E 196 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LYS E 165 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL E 198 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG E 163 " --> pdb=" O VAL E 198 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1800 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: 2.09 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3638 1.33 - 1.45: 2372 1.45 - 1.57: 7364 1.57 - 1.68: 211 1.68 - 1.80: 75 Bond restraints: 13660 Sorted by residual: bond pdb=" CB2 CDL B 402 " pdb=" C1 CDL B 402 " ideal model delta sigma weight residual 1.510 1.332 0.178 1.40e-02 5.10e+03 1.62e+02 bond pdb=" CB2 CDL C 402 " pdb=" C1 CDL C 402 " ideal model delta sigma weight residual 1.510 1.332 0.178 1.40e-02 5.10e+03 1.61e+02 bond pdb=" CB2 CDL A 402 " pdb=" C1 CDL A 402 " ideal model delta sigma weight residual 1.510 1.332 0.178 1.40e-02 5.10e+03 1.61e+02 bond pdb=" CB2 CDL E 401 " pdb=" C1 CDL E 401 " ideal model delta sigma weight residual 1.510 1.332 0.178 1.40e-02 5.10e+03 1.61e+02 bond pdb=" CB2 CDL D 402 " pdb=" C1 CDL D 402 " ideal model delta sigma weight residual 1.510 1.333 0.177 1.40e-02 5.10e+03 1.61e+02 ... (remaining 13655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 18144 3.71 - 7.43: 238 7.43 - 11.14: 48 11.14 - 14.86: 30 14.86 - 18.57: 10 Bond angle restraints: 18470 Sorted by residual: angle pdb=" C51 CDL B 402 " pdb=" CB5 CDL B 402 " pdb=" OB6 CDL B 402 " ideal model delta sigma weight residual 111.33 124.44 -13.11 1.32e+00 5.72e-01 9.84e+01 angle pdb=" C51 CDL C 402 " pdb=" CB5 CDL C 402 " pdb=" OB6 CDL C 402 " ideal model delta sigma weight residual 111.33 124.40 -13.07 1.32e+00 5.72e-01 9.78e+01 angle pdb=" C51 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 111.33 124.39 -13.06 1.32e+00 5.72e-01 9.75e+01 angle pdb=" C51 CDL D 402 " pdb=" CB5 CDL D 402 " pdb=" OB6 CDL D 402 " ideal model delta sigma weight residual 111.33 124.38 -13.05 1.32e+00 5.72e-01 9.75e+01 angle pdb=" C51 CDL E 401 " pdb=" CB5 CDL E 401 " pdb=" OB6 CDL E 401 " ideal model delta sigma weight residual 111.33 124.35 -13.02 1.32e+00 5.72e-01 9.69e+01 ... (remaining 18465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 7719 35.70 - 71.40: 306 71.40 - 107.10: 15 107.10 - 142.80: 10 142.80 - 178.50: 5 Dihedral angle restraints: 8055 sinusoidal: 3500 harmonic: 4555 Sorted by residual: dihedral pdb=" CA ILE B 79 " pdb=" C ILE B 79 " pdb=" N ASN B 80 " pdb=" CA ASN B 80 " ideal model delta harmonic sigma weight residual 180.00 150.70 29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ILE A 79 " pdb=" C ILE A 79 " pdb=" N ASN A 80 " pdb=" CA ASN A 80 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ILE C 79 " pdb=" C ILE C 79 " pdb=" N ASN C 80 " pdb=" CA ASN C 80 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 8052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1954 0.126 - 0.251: 21 0.251 - 0.377: 5 0.377 - 0.503: 5 0.503 - 0.628: 10 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA4 CDL E 401 " pdb=" CA3 CDL E 401 " pdb=" CA6 CDL E 401 " pdb=" OA6 CDL E 401 " both_signs ideal model delta sigma weight residual False -2.57 -3.20 0.63 2.00e-01 2.50e+01 9.86e+00 chirality pdb=" CA4 CDL B 402 " pdb=" CA3 CDL B 402 " pdb=" CA6 CDL B 402 " pdb=" OA6 CDL B 402 " both_signs ideal model delta sigma weight residual False -2.57 -3.20 0.63 2.00e-01 2.50e+01 9.80e+00 chirality pdb=" CA4 CDL D 402 " pdb=" CA3 CDL D 402 " pdb=" CA6 CDL D 402 " pdb=" OA6 CDL D 402 " both_signs ideal model delta sigma weight residual False -2.57 -3.20 0.63 2.00e-01 2.50e+01 9.80e+00 ... (remaining 1992 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 137 " -0.006 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASN A 137 " 0.023 2.00e-02 2.50e+03 pdb=" O ASN A 137 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN A 138 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 137 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C ASN C 137 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN C 137 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN C 138 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 137 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C ASN D 137 " -0.022 2.00e-02 2.50e+03 pdb=" O ASN D 137 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN D 138 " 0.007 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2420 2.76 - 3.30: 11624 3.30 - 3.83: 21081 3.83 - 4.37: 25506 4.37 - 4.90: 45152 Nonbonded interactions: 105783 Sorted by model distance: nonbonded pdb=" OB2 CDL D 402 " pdb=" O1 CDL D 402 " model vdw 2.227 2.432 nonbonded pdb=" OB2 CDL A 402 " pdb=" O1 CDL A 402 " model vdw 2.227 2.432 nonbonded pdb=" OB2 CDL E 401 " pdb=" O1 CDL E 401 " model vdw 2.227 2.432 nonbonded pdb=" OB2 CDL B 402 " pdb=" O1 CDL B 402 " model vdw 2.227 2.432 nonbonded pdb=" OB2 CDL C 402 " pdb=" O1 CDL C 402 " model vdw 2.227 2.432 ... (remaining 105778 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 11 through 321) selection = (chain 'B' and resid 11 through 321) selection = (chain 'C' and resid 11 through 321) selection = (chain 'D' and resid 11 through 321) selection = (chain 'E' and resid 11 through 321) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.016 0.207 13660 Z= 0.836 Angle : 1.210 18.574 18470 Z= 0.580 Chirality : 0.068 0.628 1995 Planarity : 0.003 0.029 2295 Dihedral : 17.926 178.499 5115 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.96 % Allowed : 8.27 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.20), residues: 1545 helix: -1.30 (0.20), residues: 535 sheet: 0.32 (0.26), residues: 450 loop : -2.57 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 99 TYR 0.013 0.002 TYR D 270 PHE 0.009 0.001 PHE B 78 TRP 0.010 0.001 TRP E 43 HIS 0.004 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.01603 / 0.84 (13660) covalent geometry : angle 1.20982 / 0.58 (18470) hydrogen bonds : bond 0.22491 / 14.77 ( 625) hydrogen bonds : angle 7.55312 / 5.29 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8188 (m-30) cc_final: 0.7834 (m-30) REVERT: A 87 THR cc_start: 0.9278 (t) cc_final: 0.8978 (m) REVERT: A 114 MET cc_start: 0.8987 (mtm) cc_final: 0.8607 (mtp) REVERT: A 156 GLU cc_start: 0.7957 (pm20) cc_final: 0.7699 (pm20) REVERT: A 187 GLU cc_start: 0.8050 (mt-10) cc_final: 0.6741 (pp20) REVERT: B 13 ASP cc_start: 0.8243 (m-30) cc_final: 0.7918 (m-30) REVERT: B 150 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: B 172 ASP cc_start: 0.8475 (m-30) cc_final: 0.8180 (m-30) REVERT: B 187 GLU cc_start: 0.7923 (mt-10) cc_final: 0.6629 (pp20) REVERT: C 86 ASP cc_start: 0.7952 (t70) cc_final: 0.7751 (t0) REVERT: C 114 MET cc_start: 0.9193 (mtm) cc_final: 0.8983 (mtm) REVERT: C 138 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7815 (pp30) REVERT: C 139 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: C 146 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: C 150 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6258 (mm-30) REVERT: C 172 ASP cc_start: 0.8568 (m-30) cc_final: 0.8285 (m-30) REVERT: C 185 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7429 (mp10) REVERT: C 187 GLU cc_start: 0.7752 (mt-10) cc_final: 0.6508 (pp20) REVERT: C 219 SER cc_start: 0.8664 (t) cc_final: 0.8268 (p) REVERT: D 39 ILE cc_start: 0.8584 (mt) cc_final: 0.8356 (tt) REVERT: D 150 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6378 (mm-30) REVERT: D 158 ASP cc_start: 0.7938 (m-30) cc_final: 0.7592 (m-30) REVERT: D 238 LEU cc_start: 0.8212 (mt) cc_final: 0.8008 (mt) REVERT: E 13 ASP cc_start: 0.8075 (m-30) cc_final: 0.7837 (m-30) REVERT: E 39 ILE cc_start: 0.8631 (mt) cc_final: 0.8423 (tt) REVERT: E 138 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7836 (pp30) REVERT: E 146 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: E 156 GLU cc_start: 0.7827 (pm20) cc_final: 0.7602 (pm20) REVERT: E 163 ARG cc_start: 0.8835 (mmt-90) cc_final: 0.8462 (mmp80) REVERT: E 187 GLU cc_start: 0.7900 (mt-10) cc_final: 0.6944 (pp20) REVERT: E 219 SER cc_start: 0.8664 (t) cc_final: 0.8417 (p) REVERT: E 298 GLN cc_start: 0.8031 (mt0) cc_final: 0.7774 (mt0) outliers start: 55 outliers final: 21 residues processed: 315 average time/residue: 0.6172 time to fit residues: 210.5113 Evaluate side-chains 218 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN A 137 ASN A 184 ASN A 185 GLN A 233 GLN A 284 HIS B 137 ASN B 139 GLN B 184 ASN B 185 GLN B 233 GLN C 89 ASN C 137 ASN C 139 GLN C 184 ASN C 185 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN D 27 ASN D 89 ASN D 137 ASN D 184 ASN D 185 GLN E 89 ASN E 137 ASN E 139 GLN E 184 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.126653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108577 restraints weight = 18606.392| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.87 r_work: 0.3418 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13660 Z= 0.132 Angle : 0.589 5.669 18470 Z= 0.301 Chirality : 0.046 0.145 1995 Planarity : 0.004 0.027 2295 Dihedral : 17.745 131.574 2214 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.10 % Allowed : 12.95 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.57 (0.21), residues: 1545 helix: 0.74 (0.21), residues: 515 sheet: 0.80 (0.25), residues: 450 loop : -2.46 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 65 TYR 0.017 0.001 TYR A 270 PHE 0.009 0.001 PHE E 78 TRP 0.010 0.001 TRP A 43 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (13660) covalent geometry : angle 0.58877 / 0.30 (18470) hydrogen bonds : bond 0.03771 / 2.48 ( 625) hydrogen bonds : angle 4.11643 / 2.81 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9121 (mtm) cc_final: 0.8706 (mtp) REVERT: A 156 GLU cc_start: 0.8424 (pm20) cc_final: 0.8122 (pm20) REVERT: A 187 GLU cc_start: 0.8637 (mt-10) cc_final: 0.6952 (pp20) REVERT: A 304 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: B 64 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 142 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6800 (t80) REVERT: B 146 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.6595 (mt0) REVERT: B 150 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: B 187 GLU cc_start: 0.8524 (mt-10) cc_final: 0.6877 (pp20) REVERT: B 304 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: C 114 MET cc_start: 0.9326 (mtm) cc_final: 0.9116 (mtm) REVERT: C 146 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: C 150 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: C 219 SER cc_start: 0.8756 (t) cc_final: 0.8488 (p) REVERT: C 255 ARG cc_start: 0.8285 (tpp80) cc_final: 0.8036 (tpp-160) REVERT: C 304 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: D 150 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6684 (mm-30) REVERT: D 158 ASP cc_start: 0.8388 (m-30) cc_final: 0.8067 (m-30) REVERT: D 187 GLU cc_start: 0.8602 (mt-10) cc_final: 0.6984 (pp20) REVERT: D 304 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: E 156 GLU cc_start: 0.8114 (pm20) cc_final: 0.7871 (pm20) REVERT: E 163 ARG cc_start: 0.8893 (mmt-90) cc_final: 0.8572 (mmp80) REVERT: E 245 TYR cc_start: 0.8535 (t80) cc_final: 0.8067 (t80) REVERT: E 270 TYR cc_start: 0.8228 (m-80) cc_final: 0.7367 (m-80) REVERT: E 298 GLN cc_start: 0.8210 (mt0) cc_final: 0.7985 (mt0) REVERT: E 304 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8395 (m-80) outliers start: 57 outliers final: 22 residues processed: 239 average time/residue: 0.6846 time to fit residues: 176.1311 Evaluate side-chains 188 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 50 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN A 285 HIS B 184 ASN B 284 HIS C 184 ASN C 233 GLN D 284 HIS E 184 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.108899 restraints weight = 18233.018| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.87 r_work: 0.3421 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13660 Z= 0.165 Angle : 0.583 5.769 18470 Z= 0.298 Chirality : 0.046 0.135 1995 Planarity : 0.004 0.036 2295 Dihedral : 16.562 128.950 2191 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.75 % Allowed : 13.88 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1545 helix: 1.59 (0.22), residues: 515 sheet: 0.91 (0.25), residues: 450 loop : -2.40 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 174 TYR 0.015 0.001 TYR C 245 PHE 0.010 0.001 PHE E 78 TRP 0.010 0.001 TRP E 43 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (13660) covalent geometry : angle 0.58274 / 0.30 (18470) hydrogen bonds : bond 0.03520 / 2.32 ( 625) hydrogen bonds : angle 3.87727 / 2.64 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 163 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9120 (mtm) cc_final: 0.8806 (mtp) REVERT: A 156 GLU cc_start: 0.8395 (pm20) cc_final: 0.8104 (pm20) REVERT: A 255 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8063 (tpp-160) REVERT: A 304 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: B 64 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: B 86 ASP cc_start: 0.8409 (t0) cc_final: 0.8146 (t0) REVERT: B 142 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.7065 (t80) REVERT: B 146 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.6571 (mt0) REVERT: B 150 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: B 187 GLU cc_start: 0.8596 (mt-10) cc_final: 0.6828 (pp20) REVERT: B 304 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: C 114 MET cc_start: 0.9324 (mtm) cc_final: 0.9120 (mtm) REVERT: C 150 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6724 (mm-30) REVERT: C 219 SER cc_start: 0.8787 (t) cc_final: 0.8496 (p) REVERT: C 255 ARG cc_start: 0.8257 (tpp80) cc_final: 0.8002 (tpp-160) REVERT: D 146 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.5760 (mp10) REVERT: D 150 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6857 (mm-30) REVERT: D 158 ASP cc_start: 0.8340 (m-30) cc_final: 0.8014 (m-30) REVERT: D 245 TYR cc_start: 0.8587 (t80) cc_final: 0.7964 (t80) REVERT: D 304 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: E 156 GLU cc_start: 0.8122 (pm20) cc_final: 0.7861 (pm20) REVERT: E 163 ARG cc_start: 0.8886 (mmt-90) cc_final: 0.8647 (mmp80) REVERT: E 245 TYR cc_start: 0.8580 (t80) cc_final: 0.8173 (t80) REVERT: E 298 GLN cc_start: 0.8168 (mt0) cc_final: 0.7942 (mt0) REVERT: E 304 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8337 (m-80) outliers start: 66 outliers final: 30 residues processed: 214 average time/residue: 0.6732 time to fit residues: 155.8969 Evaluate side-chains 192 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 79 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN E 200 ASN E 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109524 restraints weight = 18340.828| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.93 r_work: 0.3428 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13660 Z= 0.138 Angle : 0.562 7.805 18470 Z= 0.287 Chirality : 0.045 0.133 1995 Planarity : 0.004 0.034 2295 Dihedral : 15.399 126.424 2180 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.88 % Allowed : 15.47 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.21), residues: 1545 helix: 2.19 (0.22), residues: 495 sheet: 0.79 (0.24), residues: 480 loop : -2.28 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 174 TYR 0.014 0.001 TYR C 245 PHE 0.009 0.001 PHE E 78 TRP 0.010 0.001 TRP E 43 HIS 0.005 0.001 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13660) covalent geometry : angle 0.56167 / 0.29 (18470) hydrogen bonds : bond 0.03192 / 2.10 ( 625) hydrogen bonds : angle 3.71107 / 2.52 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9114 (mtm) cc_final: 0.8745 (mtp) REVERT: A 156 GLU cc_start: 0.8406 (pm20) cc_final: 0.8116 (pm20) REVERT: A 187 GLU cc_start: 0.8540 (mt-10) cc_final: 0.6656 (pp20) REVERT: A 255 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7998 (tpp-160) REVERT: A 279 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7842 (mm) REVERT: A 304 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: B 64 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: B 86 ASP cc_start: 0.8393 (t0) cc_final: 0.8174 (t0) REVERT: B 142 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.7129 (t80) REVERT: B 146 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.6552 (mt0) REVERT: B 150 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: B 187 GLU cc_start: 0.8419 (mt-10) cc_final: 0.6810 (pp20) REVERT: B 304 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: C 150 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: C 219 SER cc_start: 0.8785 (t) cc_final: 0.8480 (p) REVERT: C 304 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: D 146 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.5804 (mp10) REVERT: D 150 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: D 245 TYR cc_start: 0.8577 (t80) cc_final: 0.7880 (t80) REVERT: D 304 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: E 156 GLU cc_start: 0.8107 (pm20) cc_final: 0.7868 (pm20) REVERT: E 163 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8629 (mmp80) REVERT: E 245 TYR cc_start: 0.8559 (t80) cc_final: 0.8080 (t80) REVERT: E 304 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8372 (m-80) outliers start: 54 outliers final: 21 residues processed: 208 average time/residue: 0.6307 time to fit residues: 141.7820 Evaluate side-chains 189 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.0070 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 38 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 109 optimal weight: 3.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN C 285 HIS D 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.112045 restraints weight = 18163.649| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.93 r_work: 0.3463 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13660 Z= 0.098 Angle : 0.536 6.809 18470 Z= 0.273 Chirality : 0.044 0.136 1995 Planarity : 0.003 0.042 2295 Dihedral : 14.215 115.938 2171 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.38 % Allowed : 16.19 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1545 helix: 2.48 (0.23), residues: 500 sheet: 0.86 (0.24), residues: 480 loop : -2.17 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 174 TYR 0.010 0.001 TYR A 245 PHE 0.007 0.001 PHE E 78 TRP 0.009 0.001 TRP E 43 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (13660) covalent geometry : angle 0.53553 / 0.27 (18470) hydrogen bonds : bond 0.02739 / 1.81 ( 625) hydrogen bonds : angle 3.52606 / 2.38 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9070 (mtm) cc_final: 0.8784 (mtp) REVERT: A 156 GLU cc_start: 0.8447 (pm20) cc_final: 0.8214 (pm20) REVERT: A 187 GLU cc_start: 0.8509 (mt-10) cc_final: 0.6589 (pp20) REVERT: A 304 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: B 64 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: B 86 ASP cc_start: 0.8425 (t0) cc_final: 0.8171 (t0) REVERT: B 146 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.6369 (mt0) REVERT: B 150 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: B 187 GLU cc_start: 0.8331 (mt-10) cc_final: 0.6679 (pp20) REVERT: B 309 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6871 (mp) REVERT: C 219 SER cc_start: 0.8786 (t) cc_final: 0.8493 (p) REVERT: C 304 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: D 146 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.5757 (mp10) REVERT: D 150 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6831 (mm-30) REVERT: D 245 TYR cc_start: 0.8561 (t80) cc_final: 0.7893 (t80) REVERT: D 304 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: E 156 GLU cc_start: 0.8113 (pm20) cc_final: 0.7876 (pm20) REVERT: E 245 TYR cc_start: 0.8536 (t80) cc_final: 0.7538 (t80) REVERT: E 270 TYR cc_start: 0.8194 (m-80) cc_final: 0.7318 (m-80) REVERT: E 304 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8355 (m-80) outliers start: 47 outliers final: 16 residues processed: 208 average time/residue: 0.5690 time to fit residues: 128.2672 Evaluate side-chains 191 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 148 optimal weight: 2.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 233 GLN C 185 GLN C 285 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.128486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109666 restraints weight = 18251.131| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.91 r_work: 0.3429 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13660 Z= 0.165 Angle : 0.578 6.505 18470 Z= 0.296 Chirality : 0.046 0.135 1995 Planarity : 0.004 0.040 2295 Dihedral : 14.257 130.105 2166 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.67 % Allowed : 16.04 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1545 helix: 2.70 (0.22), residues: 485 sheet: 0.93 (0.24), residues: 480 loop : -2.10 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 174 TYR 0.013 0.001 TYR D 248 PHE 0.047 0.001 PHE D 247 TRP 0.008 0.001 TRP E 43 HIS 0.008 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.16 (13660) covalent geometry : angle 0.57759 / 0.30 (18470) hydrogen bonds : bond 0.03139 / 2.07 ( 625) hydrogen bonds : angle 3.64387 / 2.47 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9121 (mtm) cc_final: 0.8718 (mtp) REVERT: A 156 GLU cc_start: 0.8486 (pm20) cc_final: 0.8254 (pm20) REVERT: A 187 GLU cc_start: 0.8490 (mt-10) cc_final: 0.6677 (pp20) REVERT: A 255 ARG cc_start: 0.8322 (tpp80) cc_final: 0.7996 (tpp-160) REVERT: A 279 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8046 (mm) REVERT: A 304 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: B 64 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: B 86 ASP cc_start: 0.8441 (t0) cc_final: 0.8193 (t0) REVERT: B 142 PHE cc_start: 0.7251 (t80) cc_final: 0.6976 (t80) REVERT: B 146 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.6735 (mt0) REVERT: B 150 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: B 187 GLU cc_start: 0.8552 (mt-10) cc_final: 0.6823 (pp20) REVERT: C 219 SER cc_start: 0.8821 (t) cc_final: 0.8478 (p) REVERT: C 299 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8048 (ttm110) REVERT: C 304 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8395 (m-80) REVERT: D 146 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.5965 (mp10) REVERT: D 150 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: D 245 TYR cc_start: 0.8557 (t80) cc_final: 0.7887 (t80) REVERT: E 156 GLU cc_start: 0.8115 (pm20) cc_final: 0.7878 (pm20) REVERT: E 245 TYR cc_start: 0.8500 (t80) cc_final: 0.7787 (t80) REVERT: E 270 TYR cc_start: 0.8325 (m-80) cc_final: 0.7338 (m-80) REVERT: E 298 GLN cc_start: 0.8217 (mt0) cc_final: 0.8009 (mt0) REVERT: E 304 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8374 (m-80) outliers start: 51 outliers final: 23 residues processed: 204 average time/residue: 0.5854 time to fit residues: 129.0657 Evaluate side-chains 200 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 79 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 285 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107654 restraints weight = 18255.065| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.91 r_work: 0.3397 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13660 Z= 0.251 Angle : 0.645 6.708 18470 Z= 0.331 Chirality : 0.048 0.178 1995 Planarity : 0.004 0.068 2295 Dihedral : 14.922 148.176 2166 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.88 % Allowed : 16.26 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.22), residues: 1545 helix: 2.25 (0.22), residues: 510 sheet: 0.99 (0.25), residues: 460 loop : -2.24 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 299 TYR 0.017 0.002 TYR C 245 PHE 0.025 0.002 PHE D 247 TRP 0.010 0.001 TRP A 43 HIS 0.009 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.25 (13660) covalent geometry : angle 0.64509 / 0.33 (18470) hydrogen bonds : bond 0.03682 / 2.43 ( 625) hydrogen bonds : angle 3.82494 / 2.59 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9113 (mtm) cc_final: 0.8637 (mtp) REVERT: A 156 GLU cc_start: 0.8493 (pm20) cc_final: 0.8255 (pm20) REVERT: A 187 GLU cc_start: 0.8562 (mt-10) cc_final: 0.6750 (pp20) REVERT: A 255 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7936 (tpp-160) REVERT: A 304 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: B 64 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: B 142 PHE cc_start: 0.7235 (t80) cc_final: 0.7013 (t80) REVERT: B 146 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.6759 (mt0) REVERT: B 150 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: B 187 GLU cc_start: 0.8598 (mt-10) cc_final: 0.6880 (pp20) REVERT: C 219 SER cc_start: 0.8789 (t) cc_final: 0.8469 (p) REVERT: C 299 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8096 (ttm110) REVERT: D 146 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.6034 (mp10) REVERT: D 150 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6869 (mm-30) REVERT: D 245 TYR cc_start: 0.8600 (t80) cc_final: 0.8000 (t80) REVERT: E 156 GLU cc_start: 0.8145 (pm20) cc_final: 0.7898 (pm20) REVERT: E 245 TYR cc_start: 0.8508 (t80) cc_final: 0.8188 (t80) REVERT: E 298 GLN cc_start: 0.8176 (mt0) cc_final: 0.7950 (mt0) outliers start: 54 outliers final: 27 residues processed: 202 average time/residue: 0.6005 time to fit residues: 131.1847 Evaluate side-chains 187 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 302 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 ASN E 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.128339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109724 restraints weight = 18143.088| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.91 r_work: 0.3426 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13660 Z= 0.153 Angle : 0.597 7.764 18470 Z= 0.309 Chirality : 0.046 0.146 1995 Planarity : 0.004 0.044 2295 Dihedral : 14.188 141.441 2162 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.60 % Allowed : 16.76 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1545 helix: 2.69 (0.22), residues: 485 sheet: 1.05 (0.25), residues: 460 loop : -2.14 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 255 TYR 0.015 0.001 TYR E 248 PHE 0.047 0.002 PHE A 247 TRP 0.010 0.001 TRP E 43 HIS 0.005 0.001 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (13660) covalent geometry : angle 0.59732 / 0.31 (18470) hydrogen bonds : bond 0.03153 / 2.07 ( 625) hydrogen bonds : angle 3.66844 / 2.48 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9069 (mtm) cc_final: 0.8666 (mtp) REVERT: A 156 GLU cc_start: 0.8497 (pm20) cc_final: 0.8262 (pm20) REVERT: A 187 GLU cc_start: 0.8549 (mt-10) cc_final: 0.6742 (pp20) REVERT: A 255 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7951 (tpp-160) REVERT: A 279 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8055 (mm) REVERT: B 64 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: B 142 PHE cc_start: 0.7168 (t80) cc_final: 0.6931 (t80) REVERT: B 146 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.6599 (mt0) REVERT: B 150 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: B 187 GLU cc_start: 0.8570 (mt-10) cc_final: 0.6885 (pp20) REVERT: B 309 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7139 (mp) REVERT: C 247 PHE cc_start: 0.8013 (t80) cc_final: 0.7694 (t80) REVERT: C 299 ARG cc_start: 0.8370 (ttm-80) cc_final: 0.8085 (ttm110) REVERT: D 146 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.5889 (mp10) REVERT: D 150 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6839 (mm-30) REVERT: D 245 TYR cc_start: 0.8521 (t80) cc_final: 0.7918 (t80) REVERT: E 156 GLU cc_start: 0.8083 (pm20) cc_final: 0.7833 (pm20) REVERT: E 270 TYR cc_start: 0.8303 (m-80) cc_final: 0.7315 (m-80) REVERT: E 298 GLN cc_start: 0.8156 (mt0) cc_final: 0.7943 (mt0) REVERT: E 304 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8267 (m-80) outliers start: 50 outliers final: 22 residues processed: 195 average time/residue: 0.5697 time to fit residues: 119.8663 Evaluate side-chains 184 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 36 optimal weight: 0.0000 chunk 45 optimal weight: 0.0270 chunk 101 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.129882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111209 restraints weight = 18274.842| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.94 r_work: 0.3449 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13660 Z= 0.116 Angle : 0.583 8.245 18470 Z= 0.301 Chirality : 0.045 0.139 1995 Planarity : 0.004 0.048 2295 Dihedral : 13.550 134.763 2158 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.23 % Allowed : 18.35 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.91 (0.22), residues: 1545 helix: 2.92 (0.22), residues: 485 sheet: 0.88 (0.24), residues: 505 loop : -1.91 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 255 TYR 0.014 0.001 TYR B 245 PHE 0.021 0.001 PHE B 247 TRP 0.010 0.001 TRP A 43 HIS 0.004 0.001 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (13660) covalent geometry : angle 0.58321 / 0.30 (18470) hydrogen bonds : bond 0.02863 / 1.88 ( 625) hydrogen bonds : angle 3.54177 / 2.40 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.9032 (mtm) cc_final: 0.8687 (mtp) REVERT: A 156 GLU cc_start: 0.8491 (pm20) cc_final: 0.8265 (pm20) REVERT: A 187 GLU cc_start: 0.8501 (mt-10) cc_final: 0.6698 (pp20) REVERT: A 255 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7950 (tpp-160) REVERT: A 279 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8031 (mm) REVERT: B 64 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: B 142 PHE cc_start: 0.7060 (t80) cc_final: 0.6844 (t80) REVERT: B 146 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.6521 (mt0) REVERT: B 150 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: B 187 GLU cc_start: 0.8404 (mt-10) cc_final: 0.6879 (pp20) REVERT: B 309 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7139 (mp) REVERT: C 251 ASN cc_start: 0.8389 (t0) cc_final: 0.8108 (t0) REVERT: C 299 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.8039 (ttm110) REVERT: D 150 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: D 158 ASP cc_start: 0.8219 (m-30) cc_final: 0.7975 (m-30) REVERT: E 270 TYR cc_start: 0.8225 (m-80) cc_final: 0.7269 (m-80) outliers start: 31 outliers final: 15 residues processed: 195 average time/residue: 0.6211 time to fit residues: 131.3947 Evaluate side-chains 177 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 110 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 233 GLN C 251 ASN D 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110598 restraints weight = 18156.669| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.93 r_work: 0.3437 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13660 Z= 0.147 Angle : 0.609 8.513 18470 Z= 0.315 Chirality : 0.046 0.142 1995 Planarity : 0.005 0.111 2295 Dihedral : 13.469 136.062 2158 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.87 % Allowed : 19.14 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.22), residues: 1545 helix: 2.62 (0.23), residues: 510 sheet: 0.91 (0.24), residues: 505 loop : -1.88 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 141 TYR 0.012 0.001 TYR D 245 PHE 0.038 0.001 PHE A 247 TRP 0.011 0.001 TRP E 43 HIS 0.005 0.001 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (13660) covalent geometry : angle 0.60942 / 0.32 (18470) hydrogen bonds : bond 0.03052 / 2.01 ( 625) hydrogen bonds : angle 3.58157 / 2.43 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.9063 (mtm) cc_final: 0.8652 (mtp) REVERT: A 156 GLU cc_start: 0.8477 (pm20) cc_final: 0.8257 (pm20) REVERT: A 187 GLU cc_start: 0.8535 (mt-10) cc_final: 0.6733 (pp20) REVERT: A 247 PHE cc_start: 0.7730 (t80) cc_final: 0.7481 (t80) REVERT: A 255 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7965 (tpp-160) REVERT: B 64 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: B 146 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.6641 (mt0) REVERT: B 150 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: B 156 GLU cc_start: 0.8535 (pm20) cc_final: 0.8323 (pm20) REVERT: B 187 GLU cc_start: 0.8553 (mt-10) cc_final: 0.6872 (pp20) REVERT: B 309 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7121 (mp) REVERT: C 299 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8019 (ttm110) REVERT: D 150 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: D 158 ASP cc_start: 0.8280 (m-30) cc_final: 0.8012 (m-30) REVERT: D 304 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: E 79 ILE cc_start: 0.8498 (pp) cc_final: 0.7845 (pp) REVERT: E 270 TYR cc_start: 0.8275 (m-80) cc_final: 0.7304 (m-80) outliers start: 26 outliers final: 14 residues processed: 178 average time/residue: 0.7088 time to fit residues: 136.1506 Evaluate side-chains 175 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 77 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 102 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 ASN B 251 ASN D 138 GLN D 251 ASN E 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.130197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.111538 restraints weight = 18227.209| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.94 r_work: 0.3451 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13660 Z= 0.128 Angle : 0.600 8.747 18470 Z= 0.312 Chirality : 0.045 0.136 1995 Planarity : 0.005 0.106 2295 Dihedral : 13.024 133.684 2158 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.94 % Allowed : 19.28 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1545 helix: 2.60 (0.23), residues: 520 sheet: 0.93 (0.24), residues: 505 loop : -1.93 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 141 TYR 0.013 0.001 TYR D 245 PHE 0.021 0.001 PHE A 247 TRP 0.014 0.001 TRP E 43 HIS 0.004 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13660) covalent geometry : angle 0.60035 / 0.31 (18470) hydrogen bonds : bond 0.02889 / 1.91 ( 625) hydrogen bonds : angle 3.55036 / 2.41 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4631.88 seconds wall clock time: 79 minutes 31.24 seconds (4771.24 seconds total)