Starting phenix.real_space_refine on Thu May 15 19:25:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i41_35161/05_2025/8i41_35161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i41_35161/05_2025/8i41_35161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i41_35161/05_2025/8i41_35161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i41_35161/05_2025/8i41_35161.map" model { file = "/net/cci-nas-00/data/ceres_data/8i41_35161/05_2025/8i41_35161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i41_35161/05_2025/8i41_35161.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.001 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 25 5.49 5 S 20 5.16 5 C 8965 2.51 5 N 2030 2.21 5 O 2475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13515 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2540 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2540 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain: "C" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2540 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain: "D" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2540 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain: "E" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2540 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 163 Unusual residues: {'PLC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 47 Chain: "B" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 163 Unusual residues: {'PLC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 47 Chain: "C" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 163 Unusual residues: {'PLC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 47 Chain: "D" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 163 Unusual residues: {'PLC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 47 Chain: "E" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 163 Unusual residues: {'PLC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 47 Time building chain proxies: 7.75, per 1000 atoms: 0.57 Number of scatterers: 13515 At special positions: 0 Unit cell: (100.016, 97.888, 121.296, 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 20 16.00 P 25 15.00 O 2475 8.00 N 2030 7.00 C 8965 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: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 37.1% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.670A pdb=" N VAL A 63 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.859A pdb=" N ASP A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 removed outlier: 4.087A pdb=" N VAL A 149 " --> pdb=" O LEU A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'A' and resid 220 through 242 Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.723A pdb=" N ILE A 258 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.768A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 59 through 63 removed outlier: 3.670A pdb=" N VAL B 63 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.858A pdb=" N ASP B 122 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 removed outlier: 4.087A pdb=" N VAL B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 220 through 242 Processing helix chain 'B' and resid 253 through 282 removed outlier: 3.723A pdb=" N ILE B 258 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.769A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 59 through 63 removed outlier: 3.669A pdb=" N VAL C 63 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.858A pdb=" N ASP C 122 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 removed outlier: 4.087A pdb=" N VAL C 149 " --> pdb=" O LEU C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 215 through 218 Processing helix chain 'C' and resid 220 through 242 Processing helix chain 'C' and resid 253 through 282 removed outlier: 3.723A pdb=" N ILE C 258 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.768A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 59 through 63 removed outlier: 3.669A pdb=" N VAL D 63 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.858A pdb=" N ASP D 122 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 removed outlier: 4.088A pdb=" N VAL D 149 " --> pdb=" O LEU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'D' and resid 220 through 242 Processing helix chain 'D' and resid 253 through 282 removed outlier: 3.724A pdb=" N ILE D 258 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 259 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.769A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 59 through 63 removed outlier: 3.669A pdb=" N VAL E 63 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.859A pdb=" N ASP E 122 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 149 removed outlier: 4.087A pdb=" N VAL E 149 " --> pdb=" O LEU E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 149' Processing helix chain 'E' and resid 202 through 214 Processing helix chain 'E' and resid 215 through 218 Processing helix chain 'E' and resid 220 through 242 Processing helix chain 'E' and resid 253 through 282 removed outlier: 3.723A pdb=" N ILE E 258 " --> pdb=" O TYR E 254 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE E 259 " --> pdb=" O THR E 255 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.768A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.164A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 93 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 110 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 37 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A 38 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER A 29 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN A 40 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS A 27 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE A 42 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE A 25 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER A 44 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR A 23 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.527A pdb=" N LEU A 184 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 164 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A 191 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE A 162 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.163A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER B 93 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 110 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 37 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 38 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER B 29 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN B 40 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N CYS B 27 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE B 42 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE B 25 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER B 44 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR B 23 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.527A pdb=" N LEU B 184 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 164 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER B 191 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE B 162 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.163A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 93 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 110 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 37 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78 removed outlier: 3.527A pdb=" N LEU C 184 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 164 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER C 191 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE C 162 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.163A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER D 93 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 110 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE D 37 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 76 through 78 removed outlier: 3.527A pdb=" N LEU D 184 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER D 164 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER D 191 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE D 162 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 65 through 66 removed outlier: 6.163A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER E 93 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 110 " --> pdb=" O PHE E 37 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE E 37 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS E 38 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER E 29 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN E 40 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS E 27 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE E 42 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE E 25 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER E 44 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR E 23 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 78 removed outlier: 3.527A pdb=" N LEU E 184 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER E 164 " --> pdb=" O ARG E 189 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER E 191 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE E 162 " --> pdb=" O SER E 191 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1425 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: 3.49 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2167 1.32 - 1.44: 3699 1.44 - 1.57: 7884 1.57 - 1.69: 50 1.69 - 1.81: 35 Bond restraints: 13835 Sorted by residual: bond pdb=" C ASP D 55 " pdb=" N PRO D 56 " ideal model delta sigma weight residual 1.340 1.359 -0.019 2.76e-02 1.31e+03 4.68e-01 bond pdb=" C ASP A 55 " pdb=" N PRO A 56 " ideal model delta sigma weight residual 1.340 1.359 -0.019 2.76e-02 1.31e+03 4.68e-01 bond pdb=" C ASP E 55 " pdb=" N PRO E 56 " ideal model delta sigma weight residual 1.340 1.358 -0.018 2.76e-02 1.31e+03 4.43e-01 bond pdb=" C ASP B 55 " pdb=" N PRO B 56 " ideal model delta sigma weight residual 1.340 1.358 -0.018 2.76e-02 1.31e+03 4.31e-01 bond pdb=" C ASP C 55 " pdb=" N PRO C 56 " ideal model delta sigma weight residual 1.340 1.358 -0.018 2.76e-02 1.31e+03 4.26e-01 ... (remaining 13830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 17998 0.98 - 1.95: 575 1.95 - 2.93: 86 2.93 - 3.90: 42 3.90 - 4.88: 44 Bond angle restraints: 18745 Sorted by residual: angle pdb=" C ALA A 167 " pdb=" N VAL A 168 " pdb=" CA VAL A 168 " ideal model delta sigma weight residual 121.97 126.48 -4.51 1.80e+00 3.09e-01 6.28e+00 angle pdb=" C ALA D 167 " pdb=" N VAL D 168 " pdb=" CA VAL D 168 " ideal model delta sigma weight residual 121.97 126.44 -4.47 1.80e+00 3.09e-01 6.18e+00 angle pdb=" C ALA E 167 " pdb=" N VAL E 168 " pdb=" CA VAL E 168 " ideal model delta sigma weight residual 121.97 126.43 -4.46 1.80e+00 3.09e-01 6.14e+00 angle pdb=" C ALA C 167 " pdb=" N VAL C 168 " pdb=" CA VAL C 168 " ideal model delta sigma weight residual 121.97 126.43 -4.46 1.80e+00 3.09e-01 6.13e+00 angle pdb=" C ALA B 167 " pdb=" N VAL B 168 " pdb=" CA VAL B 168 " ideal model delta sigma weight residual 121.97 126.37 -4.40 1.80e+00 3.09e-01 5.97e+00 ... (remaining 18740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 7900 28.35 - 56.69: 390 56.69 - 85.04: 70 85.04 - 113.39: 20 113.39 - 141.74: 30 Dihedral angle restraints: 8410 sinusoidal: 3715 harmonic: 4695 Sorted by residual: dihedral pdb=" O2 PLC E 402 " pdb=" C1 PLC E 402 " pdb=" C2 PLC E 402 " pdb=" O3P PLC E 402 " ideal model delta sinusoidal sigma weight residual 304.29 162.55 141.74 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O2 PLC C 402 " pdb=" C1 PLC C 402 " pdb=" C2 PLC C 402 " pdb=" O3P PLC C 402 " ideal model delta sinusoidal sigma weight residual 304.29 162.57 141.72 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O2 PLC D 402 " pdb=" C1 PLC D 402 " pdb=" C2 PLC D 402 " pdb=" O3P PLC D 402 " ideal model delta sinusoidal sigma weight residual 304.29 162.58 141.71 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 8407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1319 0.028 - 0.057: 454 0.057 - 0.085: 218 0.085 - 0.113: 94 0.113 - 0.141: 20 Chirality restraints: 2105 Sorted by residual: chirality pdb=" CA ILE C 92 " pdb=" N ILE C 92 " pdb=" C ILE C 92 " pdb=" CB ILE C 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE B 92 " pdb=" N ILE B 92 " pdb=" C ILE B 92 " pdb=" CB ILE B 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2102 not shown) Planarity restraints: 2285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 249 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO E 250 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 250 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 250 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 249 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO D 250 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 250 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 250 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 249 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO C 250 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 250 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 250 " 0.015 5.00e-02 4.00e+02 ... (remaining 2282 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 315 2.70 - 3.25: 12775 3.25 - 3.80: 20603 3.80 - 4.35: 25078 4.35 - 4.90: 42996 Nonbonded interactions: 101767 Sorted by model distance: nonbonded pdb=" OE1 GLN C 276 " pdb=" OG1 THR C 292 " model vdw 2.152 3.040 nonbonded pdb=" OE1 GLN B 276 " pdb=" OG1 THR B 292 " model vdw 2.152 3.040 nonbonded pdb=" OE1 GLN E 276 " pdb=" OG1 THR E 292 " model vdw 2.152 3.040 nonbonded pdb=" OE1 GLN A 276 " pdb=" OG1 THR A 292 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLN D 276 " pdb=" OG1 THR D 292 " model vdw 2.153 3.040 ... (remaining 101762 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 317 or (resid 401 and (name CB or name OB or nam \ e C' or name C1 or name C1' or name C1B or name C2 or name C2' or name C2B or na \ me C3 or name C3' or name C3B or name C4' or name C4B or name C5' or name C5B or \ name C6' or name C6B or name C7' or name C8' or name O' or name O1P or name O2 \ or name O2P or name O3 or name O3P or name O4P or name P )) or resid 402 through \ 404 or (resid 405 and (name CB or name OB or name C' or name C1 or name C1' or \ name C1B or name C2 or name C2' or name C2B or name C3 or name C3' or name C3B o \ r name C4' or name C4B or name C5' or name C5B or name C6' or name C6B or name C \ 7' or name C7B or name C8' or name C8B or name C9' or name O' or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 5 through 317 or resid 401 through 402 or (resid 403 and ( \ name CB or name OB or name C' or name C1 or name C1' or name C1B or name C2 or n \ ame C2' or name C2B or name C3 or name C3' or name C3B or name C4' or name C4B o \ r name C5' or name C5B or name C6' or name C6B or name C7' or name C7B or name C \ 8' or name C8B or name C9' or name O' or name O1P or name O2 or name O2P or name \ O3 or name O3P or name O4P or name P )) or (resid 404 and (name CB or name OB o \ r name C' or name C1 or name C1' or name C1B or name C2 or name C2' or name C2B \ or name C3 or name C3' or name C3B or name C4' or name C4B or name C5' or name C \ 5B or name C6' or name C6B or name C7' or name C8' or name O' or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4P or name P )) or resid 405)) selection = (chain 'C' and (resid 5 through 317 or resid 401 through 402 or (resid 403 and ( \ name CB or name OB or name C' or name C1 or name C1' or name C1B or name C2 or n \ ame C2' or name C2B or name C3 or name C3' or name C3B or name C4' or name C4B o \ r name C5' or name C5B or name C6' or name C6B or name C7' or name C7B or name C \ 8' or name C8B or name C9' or name O' or name O1P or name O2 or name O2P or name \ O3 or name O3P or name O4P or name P )) or (resid 404 and (name CB or name OB o \ r name C' or name C1 or name C1' or name C1B or name C2 or name C2' or name C2B \ or name C3 or name C3' or name C3B or name C4' or name C4B or name C5' or name C \ 5B or name C6' or name C6B or name C7' or name C8' or name O' or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4P or name P )) or resid 405)) selection = (chain 'D' and (resid 5 through 317 or resid 401 through 402 or (resid 403 and ( \ name CB or name OB or name C' or name C1 or name C1' or name C1B or name C2 or n \ ame C2' or name C2B or name C3 or name C3' or name C3B or name C4' or name C4B o \ r name C5' or name C5B or name C6' or name C6B or name C7' or name C7B or name C \ 8' or name C8B or name C9' or name O' or name O1P or name O2 or name O2P or name \ O3 or name O3P or name O4P or name P )) or (resid 404 and (name CB or name OB o \ r name C' or name C1 or name C1' or name C1B or name C2 or name C2' or name C2B \ or name C3 or name C3' or name C3B or name C4' or name C4B or name C5' or name C \ 5B or name C6' or name C6B or name C7' or name C8' or name O' or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4P or name P )) or resid 405)) selection = (chain 'E' and (resid 5 through 317 or resid 401 through 402 or (resid 403 and ( \ name CB or name OB or name C' or name C1 or name C1' or name C1B or name C2 or n \ ame C2' or name C2B or name C3 or name C3' or name C3B or name C4' or name C4B o \ r name C5' or name C5B or name C6' or name C6B or name C7' or name C7B or name C \ 8' or name C8B or name C9' or name O' or name O1P or name O2 or name O2P or name \ O3 or name O3P or name O4P or name P )) or (resid 404 and (name CB or name OB o \ r name C' or name C1 or name C1' or name C1B or name C2 or name C2' or name C2B \ or name C3 or name C3' or name C3B or name C4' or name C4B or name C5' or name C \ 5B or name C6' or name C6B or name C7' or name C8' or name O' or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4P or name P )) or resid 405)) } 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 29.590 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.002 0.023 13835 Z= 0.095 Angle : 0.475 4.880 18745 Z= 0.243 Chirality : 0.039 0.141 2105 Planarity : 0.003 0.028 2285 Dihedral : 20.468 141.737 5350 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.36 % Allowed : 25.20 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1555 helix: 3.13 (0.21), residues: 470 sheet: -1.62 (0.26), residues: 380 loop : -2.36 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 47 HIS 0.001 0.000 HIS C 277 PHE 0.006 0.001 PHE E 238 TYR 0.011 0.001 TYR B 129 ARG 0.003 0.000 ARG E 58 Details of bonding type rmsd hydrogen bonds : bond 0.18521 ( 500) hydrogen bonds : angle 5.67340 ( 1425) covalent geometry : bond 0.00216 (13835) covalent geometry : angle 0.47474 (18745) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 1.404 Fit side-chains REVERT: A 64 LYS cc_start: 0.8198 (tptt) cc_final: 0.7763 (mtmm) REVERT: B 64 LYS cc_start: 0.8286 (tptt) cc_final: 0.7983 (mptt) REVERT: C 64 LYS cc_start: 0.8366 (tptt) cc_final: 0.7971 (mptt) REVERT: D 64 LYS cc_start: 0.8417 (tptt) cc_final: 0.8123 (mptt) REVERT: D 252 MET cc_start: 0.8470 (mmt) cc_final: 0.8265 (tpt) REVERT: E 248 LYS cc_start: 0.7972 (mmtp) cc_final: 0.7640 (mppt) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 0.3806 time to fit residues: 33.5349 Evaluate side-chains 59 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 0.0570 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 140 optimal weight: 0.0000 overall best weight: 2.7506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.128512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.088586 restraints weight = 24979.424| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.89 r_work: 0.3232 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13835 Z= 0.250 Angle : 0.616 5.372 18745 Z= 0.318 Chirality : 0.043 0.153 2105 Planarity : 0.004 0.034 2285 Dihedral : 19.603 127.278 2418 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.71 % Allowed : 23.13 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1555 helix: 2.81 (0.21), residues: 490 sheet: -1.27 (0.28), residues: 330 loop : -2.58 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 160 HIS 0.002 0.000 HIS E 127 PHE 0.016 0.002 PHE A 37 TYR 0.014 0.002 TYR C 129 ARG 0.002 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.06052 ( 500) hydrogen bonds : angle 4.86937 ( 1425) covalent geometry : bond 0.00616 (13835) covalent geometry : angle 0.61566 (18745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 LYS cc_start: 0.8661 (tptt) cc_final: 0.8309 (mptt) REVERT: D 64 LYS cc_start: 0.8724 (tptt) cc_final: 0.8410 (mptt) REVERT: E 58 ARG cc_start: 0.8040 (mmm160) cc_final: 0.6904 (tpp-160) outliers start: 24 outliers final: 12 residues processed: 82 average time/residue: 0.3607 time to fit residues: 40.4441 Evaluate side-chains 72 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain E residue 18 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 96 optimal weight: 7.9990 chunk 67 optimal weight: 0.0010 chunk 70 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.127294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086843 restraints weight = 23672.908| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.77 r_work: 0.3155 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13835 Z= 0.182 Angle : 0.545 5.340 18745 Z= 0.282 Chirality : 0.041 0.148 2105 Planarity : 0.004 0.033 2285 Dihedral : 18.018 108.430 2415 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.78 % Allowed : 22.70 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1555 helix: 3.09 (0.21), residues: 470 sheet: -1.24 (0.28), residues: 330 loop : -2.53 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 160 HIS 0.002 0.001 HIS B 277 PHE 0.011 0.001 PHE A 195 TYR 0.018 0.001 TYR D 66 ARG 0.001 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.05244 ( 500) hydrogen bonds : angle 4.53939 ( 1425) covalent geometry : bond 0.00449 (13835) covalent geometry : angle 0.54534 (18745) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 1.537 Fit side-chains REVERT: A 64 LYS cc_start: 0.8551 (tptt) cc_final: 0.8146 (mptt) REVERT: B 64 LYS cc_start: 0.8664 (tptt) cc_final: 0.8291 (mptt) REVERT: C 64 LYS cc_start: 0.8669 (tptt) cc_final: 0.8294 (mptt) REVERT: D 64 LYS cc_start: 0.8737 (tptt) cc_final: 0.8336 (mptt) REVERT: D 266 TYR cc_start: 0.8935 (m-80) cc_final: 0.8716 (m-80) REVERT: D 312 PHE cc_start: 0.8182 (t80) cc_final: 0.7628 (t80) outliers start: 39 outliers final: 16 residues processed: 98 average time/residue: 0.3143 time to fit residues: 43.6555 Evaluate side-chains 76 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 97 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.136637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089915 restraints weight = 26603.903| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.10 r_work: 0.3296 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13835 Z= 0.150 Angle : 0.530 5.253 18745 Z= 0.271 Chirality : 0.041 0.146 2105 Planarity : 0.004 0.033 2285 Dihedral : 16.672 94.193 2415 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.49 % Allowed : 22.92 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1555 helix: 3.16 (0.21), residues: 470 sheet: -1.20 (0.28), residues: 330 loop : -2.52 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 160 HIS 0.002 0.001 HIS D 277 PHE 0.010 0.001 PHE A 195 TYR 0.021 0.001 TYR A 66 ARG 0.001 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 500) hydrogen bonds : angle 4.36584 ( 1425) covalent geometry : bond 0.00368 (13835) covalent geometry : angle 0.52993 (18745) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 2.065 Fit side-chains REVERT: A 64 LYS cc_start: 0.8557 (tptt) cc_final: 0.8182 (mptt) REVERT: C 64 LYS cc_start: 0.8678 (tptt) cc_final: 0.8304 (mptt) REVERT: D 64 LYS cc_start: 0.8759 (tptt) cc_final: 0.8382 (mptt) REVERT: D 117 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8465 (ttm170) REVERT: D 312 PHE cc_start: 0.8162 (t80) cc_final: 0.7671 (t80) outliers start: 35 outliers final: 24 residues processed: 99 average time/residue: 0.4053 time to fit residues: 56.0024 Evaluate side-chains 85 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 141 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 153 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 0.0670 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.135670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089192 restraints weight = 26400.732| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.17 r_work: 0.3323 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13835 Z= 0.101 Angle : 0.500 5.113 18745 Z= 0.256 Chirality : 0.040 0.144 2105 Planarity : 0.003 0.031 2285 Dihedral : 15.337 88.451 2415 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.42 % Allowed : 23.27 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1555 helix: 3.25 (0.21), residues: 470 sheet: -1.11 (0.29), residues: 330 loop : -2.48 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 47 HIS 0.002 0.001 HIS E 277 PHE 0.007 0.001 PHE B 106 TYR 0.021 0.001 TYR E 66 ARG 0.001 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 500) hydrogen bonds : angle 4.12213 ( 1425) covalent geometry : bond 0.00239 (13835) covalent geometry : angle 0.50038 (18745) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 1.501 Fit side-chains REVERT: B 64 LYS cc_start: 0.8653 (tptt) cc_final: 0.8251 (mptt) REVERT: C 64 LYS cc_start: 0.8640 (tptt) cc_final: 0.8262 (mptt) REVERT: C 117 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8422 (ttm170) REVERT: D 38 LYS cc_start: 0.8868 (mmtm) cc_final: 0.8435 (mmmt) REVERT: D 64 LYS cc_start: 0.8813 (tptt) cc_final: 0.8394 (mptt) REVERT: D 117 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8452 (ttm170) REVERT: D 261 MET cc_start: 0.8634 (ttm) cc_final: 0.8417 (ttp) REVERT: D 266 TYR cc_start: 0.8762 (m-80) cc_final: 0.8544 (m-80) REVERT: D 312 PHE cc_start: 0.8133 (t80) cc_final: 0.7624 (t80) outliers start: 34 outliers final: 25 residues processed: 105 average time/residue: 0.3725 time to fit residues: 52.2721 Evaluate side-chains 92 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 120 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.138132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090177 restraints weight = 27307.399| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.14 r_work: 0.3215 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13835 Z= 0.156 Angle : 0.535 5.974 18745 Z= 0.273 Chirality : 0.041 0.143 2105 Planarity : 0.004 0.033 2285 Dihedral : 14.947 86.702 2415 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.20 % Allowed : 22.92 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1555 helix: 3.21 (0.21), residues: 470 sheet: -1.09 (0.29), residues: 330 loop : -2.45 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 160 HIS 0.001 0.000 HIS E 277 PHE 0.010 0.001 PHE D 195 TYR 0.012 0.001 TYR B 129 ARG 0.001 0.000 ARG D 118 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 500) hydrogen bonds : angle 4.26285 ( 1425) covalent geometry : bond 0.00385 (13835) covalent geometry : angle 0.53516 (18745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 66 time to evaluate : 1.553 Fit side-chains REVERT: A 64 LYS cc_start: 0.8554 (tptt) cc_final: 0.8164 (mptt) REVERT: A 151 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.6971 (pptt) REVERT: B 151 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6695 (pptt) REVERT: C 151 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7046 (pptt) REVERT: D 38 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8461 (mmmt) REVERT: D 151 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6953 (pptt) REVERT: D 312 PHE cc_start: 0.8184 (t80) cc_final: 0.7696 (t80) outliers start: 45 outliers final: 33 residues processed: 110 average time/residue: 0.3229 time to fit residues: 49.2658 Evaluate side-chains 99 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 132 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.140031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.093700 restraints weight = 27013.558| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.11 r_work: 0.3298 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13835 Z= 0.106 Angle : 0.510 5.966 18745 Z= 0.262 Chirality : 0.040 0.141 2105 Planarity : 0.003 0.031 2285 Dihedral : 14.393 83.243 2415 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.85 % Allowed : 22.92 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1555 helix: 3.28 (0.21), residues: 470 sheet: -0.97 (0.29), residues: 330 loop : -2.45 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.002 0.001 HIS B 127 PHE 0.008 0.001 PHE E 37 TYR 0.013 0.001 TYR D 266 ARG 0.001 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 500) hydrogen bonds : angle 4.03670 ( 1425) covalent geometry : bond 0.00250 (13835) covalent geometry : angle 0.51028 (18745) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8549 (tptt) cc_final: 0.7988 (mtmm) REVERT: A 117 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8415 (ttm170) REVERT: A 124 GLN cc_start: 0.7770 (mp10) cc_final: 0.7568 (mp10) REVERT: A 151 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.6862 (pptt) REVERT: B 64 LYS cc_start: 0.8590 (tptt) cc_final: 0.8223 (mptt) REVERT: C 64 LYS cc_start: 0.8695 (tptt) cc_final: 0.8274 (mptt) REVERT: C 117 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8482 (ttm170) REVERT: C 151 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7111 (pptt) REVERT: D 38 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8504 (mmmt) REVERT: D 64 LYS cc_start: 0.8746 (tptt) cc_final: 0.8331 (mptt) REVERT: D 117 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8461 (ttm170) REVERT: D 151 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6892 (pptt) REVERT: D 261 MET cc_start: 0.8539 (ttm) cc_final: 0.8320 (ttp) REVERT: D 312 PHE cc_start: 0.8164 (t80) cc_final: 0.7648 (t80) outliers start: 40 outliers final: 31 residues processed: 106 average time/residue: 0.3772 time to fit residues: 53.5386 Evaluate side-chains 97 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 0.0010 chunk 73 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.136133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.089154 restraints weight = 26936.863| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.13 r_work: 0.3228 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13835 Z= 0.167 Angle : 0.543 6.531 18745 Z= 0.280 Chirality : 0.041 0.142 2105 Planarity : 0.004 0.033 2285 Dihedral : 14.267 84.754 2415 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.20 % Allowed : 22.78 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1555 helix: 3.21 (0.21), residues: 470 sheet: -1.01 (0.29), residues: 330 loop : -2.41 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 160 HIS 0.002 0.001 HIS C 127 PHE 0.011 0.001 PHE B 195 TYR 0.014 0.001 TYR E 129 ARG 0.001 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04990 ( 500) hydrogen bonds : angle 4.23627 ( 1425) covalent geometry : bond 0.00411 (13835) covalent geometry : angle 0.54348 (18745) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 60 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.6892 (pptt) REVERT: B 151 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.6759 (pptt) REVERT: C 151 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7074 (pptt) REVERT: D 38 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8495 (mmmt) REVERT: D 64 LYS cc_start: 0.8729 (tptt) cc_final: 0.8399 (mptt) REVERT: D 151 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.6966 (pptt) REVERT: D 261 MET cc_start: 0.8680 (ttm) cc_final: 0.8438 (ttp) REVERT: D 312 PHE cc_start: 0.8199 (t80) cc_final: 0.7728 (t80) outliers start: 45 outliers final: 35 residues processed: 103 average time/residue: 0.3584 time to fit residues: 50.5273 Evaluate side-chains 96 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 57 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 129 optimal weight: 0.0020 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.139297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.093816 restraints weight = 26585.369| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.10 r_work: 0.3430 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13835 Z= 0.099 Angle : 0.511 6.998 18745 Z= 0.262 Chirality : 0.040 0.142 2105 Planarity : 0.003 0.031 2285 Dihedral : 13.730 85.098 2415 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.99 % Allowed : 23.27 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1555 helix: 3.30 (0.21), residues: 470 sheet: -0.94 (0.29), residues: 330 loop : -2.43 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.001 0.000 HIS E 277 PHE 0.007 0.001 PHE E 37 TYR 0.013 0.001 TYR A 266 ARG 0.001 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 500) hydrogen bonds : angle 3.95160 ( 1425) covalent geometry : bond 0.00228 (13835) covalent geometry : angle 0.51137 (18745) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 65 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8811 (mmtm) cc_final: 0.8407 (mmmt) REVERT: A 64 LYS cc_start: 0.8566 (tptt) cc_final: 0.8176 (mptt) REVERT: A 117 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8278 (ttm170) REVERT: A 151 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6886 (pptt) REVERT: B 64 LYS cc_start: 0.8593 (tptt) cc_final: 0.8247 (mptt) REVERT: B 151 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6715 (pptt) REVERT: C 64 LYS cc_start: 0.8690 (tptt) cc_final: 0.8245 (mptt) REVERT: C 117 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8486 (ttm170) REVERT: C 151 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7061 (pptt) REVERT: D 38 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8503 (mmmt) REVERT: D 64 LYS cc_start: 0.8765 (tptt) cc_final: 0.8375 (mptt) REVERT: D 117 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8433 (ttm170) REVERT: D 151 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6807 (pptt) REVERT: D 261 MET cc_start: 0.8553 (ttm) cc_final: 0.8337 (ttp) REVERT: D 284 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7075 (mt0) REVERT: D 312 PHE cc_start: 0.8172 (t80) cc_final: 0.7646 (t80) outliers start: 42 outliers final: 34 residues processed: 106 average time/residue: 0.3889 time to fit residues: 55.1057 Evaluate side-chains 102 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.138752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.093066 restraints weight = 26638.006| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.10 r_work: 0.3297 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13835 Z= 0.114 Angle : 0.512 6.484 18745 Z= 0.262 Chirality : 0.040 0.141 2105 Planarity : 0.004 0.031 2285 Dihedral : 13.452 85.766 2415 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.13 % Allowed : 23.49 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1555 helix: 3.28 (0.21), residues: 470 sheet: -0.92 (0.29), residues: 330 loop : -2.44 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.002 0.001 HIS D 127 PHE 0.007 0.001 PHE E 195 TYR 0.013 0.001 TYR A 266 ARG 0.001 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 500) hydrogen bonds : angle 3.98242 ( 1425) covalent geometry : bond 0.00278 (13835) covalent geometry : angle 0.51209 (18745) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 59 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8422 (mmmt) REVERT: A 64 LYS cc_start: 0.8541 (tptt) cc_final: 0.8139 (mptt) REVERT: A 151 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.6886 (pptt) REVERT: B 64 LYS cc_start: 0.8569 (tptt) cc_final: 0.8229 (mptt) REVERT: B 151 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6728 (pptt) REVERT: C 64 LYS cc_start: 0.8659 (tptt) cc_final: 0.8254 (mptt) REVERT: C 151 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7052 (pptt) REVERT: D 38 LYS cc_start: 0.8878 (mmtm) cc_final: 0.8527 (mmmt) REVERT: D 64 LYS cc_start: 0.8748 (tptt) cc_final: 0.8345 (mptt) REVERT: D 117 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8442 (ttm170) REVERT: D 151 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6822 (pptt) REVERT: D 261 MET cc_start: 0.8547 (ttm) cc_final: 0.8330 (ttp) REVERT: D 284 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7088 (mt0) REVERT: D 312 PHE cc_start: 0.8184 (t80) cc_final: 0.7678 (t80) outliers start: 44 outliers final: 36 residues processed: 102 average time/residue: 0.3474 time to fit residues: 48.3169 Evaluate side-chains 97 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 101 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 142 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.138225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.092082 restraints weight = 27036.052| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.11 r_work: 0.3274 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13835 Z= 0.130 Angle : 0.521 6.158 18745 Z= 0.268 Chirality : 0.040 0.141 2105 Planarity : 0.004 0.032 2285 Dihedral : 13.203 87.249 2415 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.13 % Allowed : 23.13 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1555 helix: 3.28 (0.21), residues: 470 sheet: -0.91 (0.29), residues: 330 loop : -2.42 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 160 HIS 0.003 0.001 HIS E 127 PHE 0.009 0.001 PHE D 195 TYR 0.012 0.001 TYR A 266 ARG 0.001 0.000 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 500) hydrogen bonds : angle 4.02303 ( 1425) covalent geometry : bond 0.00317 (13835) covalent geometry : angle 0.52075 (18745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6057.87 seconds wall clock time: 106 minutes 3.24 seconds (6363.24 seconds total)