Starting phenix.real_space_refine on Thu Sep 18 04:29:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l6q_23207/09_2025/7l6q_23207.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l6q_23207/09_2025/7l6q_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_23207/09_2025/7l6q_23207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l6q_23207/09_2025/7l6q_23207.map" model { file = "/net/cci-nas-00/data/ceres_data/7l6q_23207/09_2025/7l6q_23207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l6q_23207/09_2025/7l6q_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 3.79, per 1000 atoms: 0.28 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: 1.15 Conformation dependent library (CDL) restraints added in 596.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.77 Time building geometry restraints manager: 1.51 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: 7809 35.70 - 71.40: 351 71.40 - 107.10: 35 107.10 - 142.80: 20 142.80 - 178.50: 5 Dihedral angle restraints: 8220 sinusoidal: 3665 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 8217 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.090 Find NCS groups from input model: 0.330 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 19.806 178.499 5280 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 aren 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 covalent geometry : bond 0.01603 (13660) covalent geometry : angle 1.20982 (18470) hydrogen bonds : bond 0.22491 ( 625) hydrogen bonds : angle 7.55312 ( 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 : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.8189 (m-30) cc_final: 0.7835 (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: 0.7956 (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: 0.8984 (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: 0.8567 (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: 0.8585 (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: 0.8211 (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: 0.8422 (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: 0.6999 time to fit residues: 237.9098 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 : 0.537 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 D 233 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 = 0.3765 r_free = 0.3765 target = 0.126844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108780 restraints weight = 18548.565| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.86 r_work: 0.3419 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13660 Z= 0.132 Angle : 0.593 5.714 18470 Z= 0.302 Chirality : 0.046 0.157 1995 Planarity : 0.004 0.027 2295 Dihedral : 19.421 131.268 2379 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.10 % Allowed : 12.88 % Favored : 83.02 % 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 aren not related in a simple way. whole: -0.55 (0.21), residues: 1545 helix: 0.78 (0.21), residues: 515 sheet: 0.79 (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 D 43 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00307 (13660) covalent geometry : angle 0.59296 (18470) hydrogen bonds : bond 0.03656 ( 625) hydrogen bonds : angle 4.08308 ( 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 : 0.532 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: A 114 MET cc_start: 0.9120 (mtm) cc_final: 0.8702 (mtp) REVERT: A 156 GLU cc_start: 0.8431 (pm20) cc_final: 0.8130 (pm20) REVERT: A 187 GLU cc_start: 0.8635 (mt-10) cc_final: 0.6955 (pp20) REVERT: A 304 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: B 64 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: B 142 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6796 (t80) REVERT: B 146 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.6609 (mt0) REVERT: B 150 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: B 187 GLU cc_start: 0.8525 (mt-10) cc_final: 0.6877 (pp20) REVERT: C 114 MET cc_start: 0.9326 (mtm) cc_final: 0.9115 (mtm) REVERT: C 150 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: C 219 SER cc_start: 0.8754 (t) cc_final: 0.8486 (p) REVERT: C 255 ARG cc_start: 0.8284 (tpp80) cc_final: 0.8039 (tpp-160) REVERT: C 304 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: D 150 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6682 (mm-30) REVERT: D 158 ASP cc_start: 0.8391 (m-30) cc_final: 0.8070 (m-30) REVERT: D 187 GLU cc_start: 0.8598 (mt-10) cc_final: 0.6977 (pp20) REVERT: E 156 GLU cc_start: 0.8117 (pm20) cc_final: 0.7875 (pm20) REVERT: E 163 ARG cc_start: 0.8893 (mmt-90) cc_final: 0.8573 (mmp80) REVERT: E 245 TYR cc_start: 0.8529 (t80) cc_final: 0.8089 (t80) REVERT: E 270 TYR cc_start: 0.8212 (m-80) cc_final: 0.7372 (m-80) REVERT: E 298 GLN cc_start: 0.8222 (mt0) cc_final: 0.8009 (mt0) REVERT: E 304 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8393 (m-80) outliers start: 57 outliers final: 21 residues processed: 239 average time/residue: 0.7887 time to fit residues: 202.0543 Evaluate side-chains 187 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 141 ARG 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 142 PHE Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 300 CYS 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: 1.9990 chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 285 HIS B 184 ASN B 284 HIS C 89 ASN C 184 ASN C 233 GLN C 298 GLN D 233 GLN D 284 HIS E 184 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108113 restraints weight = 18296.002| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.91 r_work: 0.3401 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2142 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= 0.177 Angle : 0.591 5.818 18470 Z= 0.302 Chirality : 0.046 0.136 1995 Planarity : 0.004 0.039 2295 Dihedral : 17.559 130.429 2345 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.60 % Allowed : 14.03 % 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 aren not related in a simple way. whole: -0.05 (0.21), residues: 1545 helix: 1.56 (0.22), residues: 515 sheet: 0.90 (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 0.009 0.001 PHE E 78 TRP 0.011 0.001 TRP E 43 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00435 (13660) covalent geometry : angle 0.59096 (18470) hydrogen bonds : bond 0.03575 ( 625) hydrogen bonds : angle 3.89785 ( 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 225 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 161 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9105 (mtm) cc_final: 0.8671 (mtp) REVERT: A 156 GLU cc_start: 0.8447 (pm20) cc_final: 0.8159 (pm20) REVERT: A 255 ARG cc_start: 0.8282 (tpp80) cc_final: 0.7987 (tpp-160) REVERT: A 304 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: B 64 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: B 86 ASP cc_start: 0.8401 (t0) cc_final: 0.8147 (t0) REVERT: B 146 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.6623 (mt0) REVERT: B 150 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: B 187 GLU cc_start: 0.8563 (mt-10) cc_final: 0.6835 (pp20) REVERT: C 150 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: C 219 SER cc_start: 0.8771 (t) cc_final: 0.8478 (p) REVERT: C 255 ARG cc_start: 0.8266 (tpp80) cc_final: 0.8001 (tpp-160) REVERT: D 146 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.5755 (mp10) REVERT: D 150 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: D 158 ASP cc_start: 0.8347 (m-30) cc_final: 0.8021 (m-30) REVERT: D 245 TYR cc_start: 0.8607 (t80) cc_final: 0.7980 (t80) REVERT: E 156 GLU cc_start: 0.8096 (pm20) cc_final: 0.7836 (pm20) REVERT: E 163 ARG cc_start: 0.8901 (mmt-90) cc_final: 0.8669 (mmp80) REVERT: E 245 TYR cc_start: 0.8546 (t80) cc_final: 0.8202 (t80) REVERT: E 298 GLN cc_start: 0.8137 (mt0) cc_final: 0.7925 (mt0) REVERT: E 304 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8330 (m-80) outliers start: 64 outliers final: 28 residues processed: 209 average time/residue: 0.7527 time to fit residues: 169.2625 Evaluate side-chains 187 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 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 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 141 ARG 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 300 CYS 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 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: 0.0670 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 200 ASN E 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.109612 restraints weight = 18351.573| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.93 r_work: 0.3431 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2378 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= 0.131 Angle : 0.562 7.810 18470 Z= 0.287 Chirality : 0.045 0.132 1995 Planarity : 0.004 0.035 2295 Dihedral : 16.121 126.458 2341 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.67 % Allowed : 15.54 % Favored : 80.79 % 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 aren not related in a simple way. whole: 0.29 (0.21), residues: 1545 helix: 2.20 (0.22), residues: 495 sheet: 0.79 (0.24), residues: 480 loop : -2.29 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 174 TYR 0.014 0.001 TYR C 245 PHE 0.010 0.001 PHE E 78 TRP 0.010 0.001 TRP A 43 HIS 0.005 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00314 (13660) covalent geometry : angle 0.56237 (18470) hydrogen bonds : bond 0.03133 ( 625) hydrogen bonds : angle 3.69935 ( 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 217 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9112 (mtm) cc_final: 0.8756 (mtp) REVERT: A 156 GLU cc_start: 0.8413 (pm20) cc_final: 0.8123 (pm20) REVERT: A 255 ARG cc_start: 0.8285 (tpp80) cc_final: 0.7993 (tpp-160) REVERT: A 279 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7842 (mm) REVERT: A 304 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: B 64 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 86 ASP cc_start: 0.8408 (t0) cc_final: 0.8197 (t0) REVERT: B 142 PHE cc_start: 0.7319 (t80) cc_final: 0.7071 (t80) REVERT: B 146 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.6538 (mt0) REVERT: B 150 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: B 187 GLU cc_start: 0.8419 (mt-10) cc_final: 0.6796 (pp20) REVERT: C 219 SER cc_start: 0.8789 (t) cc_final: 0.8479 (p) REVERT: C 304 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: D 146 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.5812 (mp10) REVERT: D 150 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6869 (mm-30) REVERT: D 158 ASP cc_start: 0.8337 (m-30) cc_final: 0.8006 (m-30) REVERT: D 245 TYR cc_start: 0.8577 (t80) cc_final: 0.7889 (t80) REVERT: E 86 ASP cc_start: 0.8405 (t0) cc_final: 0.8202 (t0) REVERT: E 156 GLU cc_start: 0.8100 (pm20) cc_final: 0.7863 (pm20) REVERT: E 163 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8636 (mmp80) REVERT: E 245 TYR cc_start: 0.8565 (t80) cc_final: 0.8089 (t80) REVERT: E 304 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8373 (m-80) outliers start: 51 outliers final: 18 residues processed: 204 average time/residue: 0.7429 time to fit residues: 163.3436 Evaluate side-chains 184 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS 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 87 THR 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 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 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: 0.9980 chunk 32 optimal weight: 0.0010 chunk 86 optimal weight: 0.2980 chunk 38 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 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 = 0.3801 r_free = 0.3801 target = 0.129858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.111126 restraints weight = 18159.502| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.92 r_work: 0.3451 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2619 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= 0.112 Angle : 0.548 6.711 18470 Z= 0.279 Chirality : 0.045 0.134 1995 Planarity : 0.003 0.040 2295 Dihedral : 15.026 122.877 2329 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.38 % Allowed : 16.33 % 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 aren not related in a simple way. whole: 0.54 (0.22), residues: 1545 helix: 2.51 (0.23), residues: 495 sheet: 0.88 (0.24), residues: 480 loop : -2.21 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 174 TYR 0.013 0.001 TYR A 245 PHE 0.008 0.001 PHE E 78 TRP 0.009 0.001 TRP A 43 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00262 (13660) covalent geometry : angle 0.54795 (18470) hydrogen bonds : bond 0.02865 ( 625) hydrogen bonds : angle 3.55999 ( 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 215 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9088 (mtm) cc_final: 0.8771 (mtp) REVERT: A 156 GLU cc_start: 0.8445 (pm20) cc_final: 0.8210 (pm20) REVERT: A 304 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: B 64 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: B 86 ASP cc_start: 0.8431 (t0) cc_final: 0.8188 (t0) REVERT: B 142 PHE cc_start: 0.7330 (t80) cc_final: 0.7108 (t80) REVERT: B 146 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6486 (mt0) REVERT: B 150 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: B 187 GLU cc_start: 0.8524 (mt-10) cc_final: 0.6731 (pp20) REVERT: B 309 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6940 (mp) REVERT: C 219 SER cc_start: 0.8786 (t) cc_final: 0.8477 (p) REVERT: C 304 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: D 146 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.5800 (mp10) REVERT: D 150 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6837 (mm-30) REVERT: D 158 ASP cc_start: 0.8239 (m-30) cc_final: 0.7915 (m-30) REVERT: D 245 TYR cc_start: 0.8546 (t80) cc_final: 0.7853 (t80) REVERT: E 86 ASP cc_start: 0.8413 (t0) cc_final: 0.8183 (t0) REVERT: E 156 GLU cc_start: 0.8101 (pm20) cc_final: 0.7868 (pm20) REVERT: E 245 TYR cc_start: 0.8551 (t80) cc_final: 0.7910 (t80) REVERT: E 270 TYR cc_start: 0.8249 (m-80) cc_final: 0.7293 (m-80) outliers start: 47 outliers final: 18 residues processed: 203 average time/residue: 0.7148 time to fit residues: 156.8371 Evaluate side-chains 189 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS 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 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 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 300 CYS Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 0.0170 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 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 = 0.3787 r_free = 0.3787 target = 0.128525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110435 restraints weight = 18523.814| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.88 r_work: 0.3443 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13660 Z= 0.117 Angle : 0.552 6.326 18470 Z= 0.282 Chirality : 0.045 0.132 1995 Planarity : 0.004 0.056 2295 Dihedral : 14.509 125.604 2327 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.17 % Allowed : 16.76 % Favored : 80.07 % 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 aren not related in a simple way. whole: 0.67 (0.22), residues: 1545 helix: 2.68 (0.22), residues: 495 sheet: 0.93 (0.24), residues: 480 loop : -2.17 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 174 TYR 0.014 0.001 TYR A 245 PHE 0.047 0.001 PHE D 247 TRP 0.009 0.001 TRP A 43 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00278 (13660) covalent geometry : angle 0.55151 (18470) hydrogen bonds : bond 0.02789 ( 625) hydrogen bonds : angle 3.53135 ( 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 204 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9081 (mtm) cc_final: 0.8723 (mtp) REVERT: A 156 GLU cc_start: 0.8487 (pm20) cc_final: 0.8250 (pm20) REVERT: A 187 GLU cc_start: 0.8550 (mt-10) cc_final: 0.6680 (pp20) REVERT: A 279 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7930 (mm) REVERT: A 304 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: B 64 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: B 86 ASP cc_start: 0.8444 (t0) cc_final: 0.8202 (t0) REVERT: B 142 PHE cc_start: 0.7208 (t80) cc_final: 0.6951 (t80) REVERT: B 146 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.6580 (mt0) REVERT: B 150 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: B 156 GLU cc_start: 0.8494 (pm20) cc_final: 0.8214 (pm20) REVERT: B 309 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7034 (mp) REVERT: C 219 SER cc_start: 0.8777 (t) cc_final: 0.8521 (p) REVERT: C 299 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.8037 (ttm110) REVERT: C 304 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: D 146 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.5834 (mp10) REVERT: D 150 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: D 245 TYR cc_start: 0.8488 (t80) cc_final: 0.7845 (t80) REVERT: E 86 ASP cc_start: 0.8389 (t0) cc_final: 0.8124 (t0) REVERT: E 156 GLU cc_start: 0.8139 (pm20) cc_final: 0.7903 (pm20) REVERT: E 245 TYR cc_start: 0.8438 (t80) cc_final: 0.7359 (t80) REVERT: E 270 TYR cc_start: 0.8270 (m-80) cc_final: 0.7307 (m-80) REVERT: E 304 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8387 (m-80) outliers start: 44 outliers final: 21 residues processed: 192 average time/residue: 0.7193 time to fit residues: 149.0633 Evaluate side-chains 189 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 87 THR Chi-restraints excluded: chain B residue 113 ASP 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 87 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 286 ARG 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 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 300 CYS Chi-restraints excluded: chain E residue 29 LEU 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: 0.5980 chunk 59 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.112199 restraints weight = 18155.101| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.90 r_work: 0.3461 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13660 Z= 0.116 Angle : 0.560 7.094 18470 Z= 0.287 Chirality : 0.044 0.131 1995 Planarity : 0.004 0.059 2295 Dihedral : 14.130 126.648 2327 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.74 % Allowed : 16.62 % 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 aren not related in a simple way. whole: 0.86 (0.22), residues: 1545 helix: 2.93 (0.22), residues: 485 sheet: 0.81 (0.24), residues: 505 loop : -1.95 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 299 TYR 0.018 0.001 TYR A 245 PHE 0.031 0.001 PHE D 247 TRP 0.009 0.001 TRP D 43 HIS 0.007 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00271 (13660) covalent geometry : angle 0.56049 (18470) hydrogen bonds : bond 0.02743 ( 625) hydrogen bonds : angle 3.49379 ( 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 218 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7978 (mttp) REVERT: A 114 MET cc_start: 0.9060 (mtm) cc_final: 0.8729 (mtp) REVERT: A 156 GLU cc_start: 0.8495 (pm20) cc_final: 0.8268 (pm20) REVERT: A 187 GLU cc_start: 0.8459 (mt-10) cc_final: 0.6680 (pp20) REVERT: A 255 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7966 (tpp-160) REVERT: A 279 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8002 (mm) REVERT: B 61 THR cc_start: 0.8740 (m) cc_final: 0.8533 (m) REVERT: B 64 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: B 142 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6984 (t80) REVERT: B 146 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6568 (mt0) REVERT: B 150 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: B 156 GLU cc_start: 0.8503 (pm20) cc_final: 0.8284 (pm20) REVERT: B 187 GLU cc_start: 0.8314 (mt-10) cc_final: 0.6737 (pp20) REVERT: B 309 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7040 (mp) REVERT: C 219 SER cc_start: 0.8727 (t) cc_final: 0.8458 (p) REVERT: C 299 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.8040 (ttm110) REVERT: D 150 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: E 156 GLU cc_start: 0.8091 (pm20) cc_final: 0.7875 (pm20) REVERT: E 270 TYR cc_start: 0.8230 (m-80) cc_final: 0.7268 (m-80) REVERT: E 304 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8332 (m-80) outliers start: 52 outliers final: 19 residues processed: 203 average time/residue: 0.6922 time to fit residues: 151.4278 Evaluate side-chains 188 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 109 SER 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 87 THR Chi-restraints excluded: chain B residue 113 ASP 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 309 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 142 PHE 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 E residue 29 LEU 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=2.00 ------------------------------------------------------------------------------- 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: 0.9980 chunk 120 optimal weight: 0.0040 chunk 128 optimal weight: 0.0270 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 0.0270 chunk 61 optimal weight: 3.9990 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN D 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.131881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.113430 restraints weight = 18163.489| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.91 r_work: 0.3476 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13660 Z= 0.104 Angle : 0.554 7.688 18470 Z= 0.283 Chirality : 0.044 0.133 1995 Planarity : 0.004 0.044 2295 Dihedral : 13.546 123.762 2323 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.66 % Allowed : 17.48 % 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 aren not related in a simple way. whole: 0.98 (0.22), residues: 1545 helix: 3.04 (0.22), residues: 485 sheet: 0.87 (0.24), residues: 505 loop : -1.89 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 299 TYR 0.017 0.001 TYR A 245 PHE 0.014 0.001 PHE D 247 TRP 0.009 0.001 TRP A 43 HIS 0.005 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00238 (13660) covalent geometry : angle 0.55395 (18470) hydrogen bonds : bond 0.02624 ( 625) hydrogen bonds : angle 3.45501 ( 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 204 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.569 Fit side-chains REVERT: A 34 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8018 (mttp) REVERT: A 114 MET cc_start: 0.9035 (mtm) cc_final: 0.8748 (mtp) REVERT: A 156 GLU cc_start: 0.8468 (pm20) cc_final: 0.8238 (pm20) REVERT: A 187 GLU cc_start: 0.8437 (mt-10) cc_final: 0.6666 (pp20) REVERT: B 61 THR cc_start: 0.8636 (m) cc_final: 0.8374 (m) REVERT: B 64 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: B 146 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.6528 (mt0) REVERT: B 150 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: B 156 GLU cc_start: 0.8491 (pm20) cc_final: 0.8117 (pm20) REVERT: B 309 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7042 (mp) REVERT: C 219 SER cc_start: 0.8748 (t) cc_final: 0.8481 (p) REVERT: C 299 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.8013 (ttm110) REVERT: D 150 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: D 187 GLU cc_start: 0.8586 (mt-10) cc_final: 0.6961 (pp20) REVERT: E 245 TYR cc_start: 0.8475 (t80) cc_final: 0.7428 (t80) REVERT: E 270 TYR cc_start: 0.8188 (m-80) cc_final: 0.7281 (m-80) REVERT: E 304 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8349 (m-80) outliers start: 37 outliers final: 17 residues processed: 190 average time/residue: 0.7125 time to fit residues: 145.9968 Evaluate side-chains 186 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 109 SER 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 113 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU 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 279 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 138 GLN 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 300 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 36 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 101 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.112143 restraints weight = 18316.277| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.93 r_work: 0.3461 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13660 Z= 0.124 Angle : 0.574 8.167 18470 Z= 0.293 Chirality : 0.045 0.141 1995 Planarity : 0.004 0.050 2295 Dihedral : 13.460 125.509 2323 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.37 % Allowed : 18.13 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.22), residues: 1545 helix: 2.65 (0.23), residues: 520 sheet: 0.90 (0.24), residues: 505 loop : -2.00 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 255 TYR 0.015 0.001 TYR C 248 PHE 0.038 0.001 PHE D 247 TRP 0.008 0.001 TRP A 43 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00295 (13660) covalent geometry : angle 0.57422 (18470) hydrogen bonds : bond 0.02747 ( 625) hydrogen bonds : angle 3.50967 ( 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 197 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.532 Fit side-chains REVERT: A 34 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.7978 (mttp) REVERT: A 114 MET cc_start: 0.9062 (mtm) cc_final: 0.8720 (mtp) REVERT: A 156 GLU cc_start: 0.8472 (pm20) cc_final: 0.8249 (pm20) REVERT: A 187 GLU cc_start: 0.8445 (mt-10) cc_final: 0.6659 (pp20) REVERT: A 255 ARG cc_start: 0.8285 (tpp80) cc_final: 0.7942 (tpp-160) REVERT: B 61 THR cc_start: 0.8734 (m) cc_final: 0.8480 (m) REVERT: B 64 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 146 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.6585 (mt0) REVERT: B 150 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: B 156 GLU cc_start: 0.8495 (pm20) cc_final: 0.8220 (pm20) REVERT: B 187 GLU cc_start: 0.8449 (mt-10) cc_final: 0.6706 (pp20) REVERT: B 286 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6624 (ptm-80) REVERT: B 309 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7168 (mp) REVERT: C 219 SER cc_start: 0.8722 (t) cc_final: 0.8444 (p) REVERT: C 299 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.8028 (ttm110) REVERT: D 150 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: E 270 TYR cc_start: 0.8244 (m-80) cc_final: 0.7239 (m-80) REVERT: E 304 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8355 (m-80) outliers start: 33 outliers final: 19 residues processed: 188 average time/residue: 0.7475 time to fit residues: 151.5080 Evaluate side-chains 194 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 300 CYS 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 113 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 286 ARG 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 279 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 138 GLN 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 300 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 110 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 154 optimal weight: 0.0470 chunk 70 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN C 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109986 restraints weight = 18217.476| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.92 r_work: 0.3427 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13660 Z= 0.189 Angle : 0.624 8.422 18470 Z= 0.320 Chirality : 0.047 0.148 1995 Planarity : 0.004 0.058 2295 Dihedral : 13.942 135.245 2323 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.94 % Allowed : 18.71 % Favored : 79.35 % 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 aren not related in a simple way. whole: 0.85 (0.22), residues: 1545 helix: 2.61 (0.22), residues: 510 sheet: 0.88 (0.24), residues: 505 loop : -1.93 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 255 TYR 0.019 0.002 TYR E 248 PHE 0.049 0.002 PHE C 247 TRP 0.007 0.001 TRP D 206 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00466 (13660) covalent geometry : angle 0.62414 (18470) hydrogen bonds : bond 0.03203 ( 625) hydrogen bonds : angle 3.64064 ( 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 194 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.487 Fit side-chains REVERT: A 34 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8310 (mttp) REVERT: A 114 MET cc_start: 0.9108 (mtm) cc_final: 0.8674 (mtp) REVERT: A 156 GLU cc_start: 0.8482 (pm20) cc_final: 0.8258 (pm20) REVERT: A 187 GLU cc_start: 0.8469 (mt-10) cc_final: 0.6689 (pp20) REVERT: A 255 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7965 (tpp-160) REVERT: B 61 THR cc_start: 0.8761 (m) cc_final: 0.8511 (m) REVERT: B 64 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: B 146 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.6768 (mt0) REVERT: B 150 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: B 187 GLU cc_start: 0.8489 (mt-10) cc_final: 0.6849 (pp20) REVERT: B 286 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6598 (ptm-80) REVERT: C 219 SER cc_start: 0.8754 (t) cc_final: 0.8493 (p) REVERT: C 299 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8067 (ttm110) REVERT: D 150 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: E 245 TYR cc_start: 0.8483 (t80) cc_final: 0.8005 (t80) REVERT: E 270 TYR cc_start: 0.8315 (m-80) cc_final: 0.7292 (m-80) REVERT: E 304 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8358 (m-80) outliers start: 27 outliers final: 17 residues processed: 185 average time/residue: 0.7390 time to fit residues: 147.2817 Evaluate side-chains 191 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 109 SER 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 113 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 286 ARG 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 138 GLN 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 300 CYS Chi-restraints excluded: chain E residue 141 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 77 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 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 = 0.3800 r_free = 0.3800 target = 0.129963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111137 restraints weight = 18253.703| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.97 r_work: 0.3444 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13660 Z= 0.139 Angle : 0.597 8.752 18470 Z= 0.307 Chirality : 0.046 0.187 1995 Planarity : 0.004 0.059 2295 Dihedral : 13.647 133.554 2323 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.30 % Allowed : 18.78 % Favored : 78.92 % 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 aren not related in a simple way. whole: 0.85 (0.22), residues: 1545 helix: 2.55 (0.23), residues: 520 sheet: 0.92 (0.24), residues: 505 loop : -2.01 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 299 TYR 0.016 0.001 TYR C 248 PHE 0.047 0.001 PHE E 247 TRP 0.008 0.001 TRP A 43 HIS 0.007 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00334 (13660) covalent geometry : angle 0.59677 (18470) hydrogen bonds : bond 0.02934 ( 625) hydrogen bonds : angle 3.56648 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5218.87 seconds wall clock time: 89 minutes 30.14 seconds (5370.14 seconds total)