Starting phenix.real_space_refine on Thu Jun 12 03:28:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i41_35161/06_2025/8i41_35161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i41_35161/06_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_35161/06_2025/8i41_35161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i41_35161/06_2025/8i41_35161.map" model { file = "/net/cci-nas-00/data/ceres_data/8i41_35161/06_2025/8i41_35161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i41_35161/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.79, per 1000 atoms: 0.65 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: 3.57 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: 1.22 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: 3.45 Time building geometry restraints manager: 4.18 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: 1.170 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.410 Find NCS groups from input model: 0.670 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- 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 : 1.722 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: 0.4032 time to fit residues: 36.3793 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 : 1.648 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.136110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089737 restraints weight = 26653.021| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.08 r_work: 0.3341 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 19.603 127.276 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 4.86938 ( 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 : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 LYS cc_start: 0.8694 (tptt) cc_final: 0.8318 (mptt) REVERT: D 64 LYS cc_start: 0.8750 (tptt) cc_final: 0.8415 (mptt) REVERT: E 58 ARG cc_start: 0.8032 (mmm160) cc_final: 0.6888 (tpp-160) outliers start: 24 outliers final: 12 residues processed: 82 average time/residue: 0.4417 time to fit residues: 49.8842 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 : 1.384 ------------------------------------------------------------------------------- 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: 0.0040 chunk 70 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.126764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086149 restraints weight = 23716.574| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.80 r_work: 0.3136 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13835 Z= 0.197 Angle : 0.557 5.430 18745 Z= 0.289 Chirality : 0.042 0.146 2105 Planarity : 0.004 0.034 2285 Dihedral : 18.001 107.060 2415 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.27 % Allowed : 22.63 % Favored : 74.09 % 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: -0.70 (0.21), residues: 1555 helix: 3.06 (0.21), residues: 470 sheet: -1.28 (0.28), residues: 330 loop : -2.54 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 160 HIS 0.002 0.001 HIS B 277 PHE 0.011 0.001 PHE A 195 TYR 0.020 0.001 TYR D 66 ARG 0.001 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.05429 ( 500) hydrogen bonds : angle 4.57401 ( 1425) covalent geometry : bond 0.00488 (13835) covalent geometry : angle 0.55697 (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 109 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 63 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: B 64 LYS cc_start: 0.8637 (tptt) cc_final: 0.8277 (mptt) REVERT: C 64 LYS cc_start: 0.8677 (tptt) cc_final: 0.8299 (mptt) REVERT: D 64 LYS cc_start: 0.8735 (tptt) cc_final: 0.8360 (mptt) REVERT: D 266 TYR cc_start: 0.8933 (m-80) cc_final: 0.8719 (m-80) REVERT: D 312 PHE cc_start: 0.8214 (t80) cc_final: 0.7679 (t80) REVERT: E 248 LYS cc_start: 0.7989 (mmtp) cc_final: 0.7686 (mppt) outliers start: 46 outliers final: 22 residues processed: 102 average time/residue: 0.3278 time to fit residues: 46.8440 Evaluate side-chains 81 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 76 ILE 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 20 THR 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 76 ILE 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 20 THR 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: 0.7980 chunk 126 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4140 r_free = 0.4140 target = 0.138408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.092899 restraints weight = 26546.452| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.09 r_work: 0.3285 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13835 Z= 0.116 Angle : 0.513 6.383 18745 Z= 0.262 Chirality : 0.041 0.146 2105 Planarity : 0.004 0.032 2285 Dihedral : 16.564 93.719 2415 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.21 % Allowed : 23.27 % 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: -0.57 (0.21), residues: 1555 helix: 3.23 (0.21), residues: 470 sheet: -1.20 (0.28), residues: 330 loop : -2.51 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 213 HIS 0.002 0.001 HIS B 277 PHE 0.008 0.001 PHE A 195 TYR 0.019 0.001 TYR A 66 ARG 0.001 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 500) hydrogen bonds : angle 4.25133 ( 1425) covalent geometry : bond 0.00279 (13835) covalent geometry : angle 0.51317 (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 101 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 2.250 Fit side-chains REVERT: A 64 LYS cc_start: 0.8597 (tptt) cc_final: 0.8183 (mptt) REVERT: C 64 LYS cc_start: 0.8664 (tptt) cc_final: 0.8286 (mptt) REVERT: C 117 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8458 (ttm170) REVERT: D 38 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8495 (mmmt) REVERT: D 64 LYS cc_start: 0.8770 (tptt) cc_final: 0.8374 (mptt) REVERT: D 312 PHE cc_start: 0.8164 (t80) cc_final: 0.7666 (t80) outliers start: 31 outliers final: 21 residues processed: 98 average time/residue: 0.5781 time to fit residues: 77.9375 Evaluate side-chains 88 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 271 ILE 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 58 ARG 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 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 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 18 VAL 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: 4.9990 chunk 148 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.138445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092911 restraints weight = 26817.525| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.10 r_work: 0.3319 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13835 Z= 0.116 Angle : 0.520 6.960 18745 Z= 0.263 Chirality : 0.040 0.143 2105 Planarity : 0.004 0.031 2285 Dihedral : 15.454 88.791 2415 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.35 % Allowed : 23.84 % Favored : 73.81 % 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: 3.24 (0.21), residues: 470 sheet: -1.13 (0.28), residues: 330 loop : -2.46 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 160 HIS 0.001 0.001 HIS E 127 PHE 0.008 0.001 PHE A 195 TYR 0.017 0.001 TYR D 266 ARG 0.001 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 500) hydrogen bonds : angle 4.17733 ( 1425) covalent geometry : bond 0.00280 (13835) covalent geometry : angle 0.51989 (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 102 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 3.506 Fit side-chains REVERT: A 117 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8444 (ttm170) REVERT: A 151 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.6935 (pptt) REVERT: B 64 LYS cc_start: 0.8600 (tptt) cc_final: 0.8238 (mptt) REVERT: C 64 LYS cc_start: 0.8621 (tptt) cc_final: 0.8260 (mptt) REVERT: D 64 LYS cc_start: 0.8768 (tptt) cc_final: 0.8321 (mptt) REVERT: D 151 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6950 (pptt) REVERT: D 261 MET cc_start: 0.8541 (ttm) cc_final: 0.8325 (ttp) REVERT: D 266 TYR cc_start: 0.8799 (m-80) cc_final: 0.8592 (m-80) REVERT: D 312 PHE cc_start: 0.8163 (t80) cc_final: 0.7691 (t80) outliers start: 33 outliers final: 22 residues processed: 99 average time/residue: 0.5688 time to fit residues: 76.4678 Evaluate side-chains 89 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG 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 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 58 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 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain E residue 18 VAL 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: 0.8980 chunk 2 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.139053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.092248 restraints weight = 27229.545| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.13 r_work: 0.3302 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13835 Z= 0.132 Angle : 0.517 6.091 18745 Z= 0.265 Chirality : 0.041 0.144 2105 Planarity : 0.004 0.032 2285 Dihedral : 14.782 85.618 2415 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.63 % Allowed : 23.56 % Favored : 73.81 % 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: -0.47 (0.21), residues: 1555 helix: 3.24 (0.21), residues: 470 sheet: -1.09 (0.28), residues: 330 loop : -2.43 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 160 HIS 0.001 0.001 HIS E 277 PHE 0.009 0.001 PHE D 195 TYR 0.012 0.001 TYR E 129 ARG 0.001 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 500) hydrogen bonds : angle 4.16802 ( 1425) covalent geometry : bond 0.00322 (13835) covalent geometry : angle 0.51730 (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 102 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 5.161 Fit side-chains REVERT: A 64 LYS cc_start: 0.8520 (tptt) cc_final: 0.8133 (mptt) REVERT: B 64 LYS cc_start: 0.8611 (tptt) cc_final: 0.8209 (mptt) REVERT: B 151 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6726 (pptt) REVERT: C 117 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8496 (ttm170) REVERT: C 151 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7102 (pptt) REVERT: D 38 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8543 (mmmt) REVERT: D 261 MET cc_start: 0.8587 (ttm) cc_final: 0.8361 (ttp) REVERT: D 312 PHE cc_start: 0.8186 (t80) cc_final: 0.7721 (t80) outliers start: 37 outliers final: 26 residues processed: 100 average time/residue: 0.6997 time to fit residues: 96.3373 Evaluate side-chains 91 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 169 VAL Chi-restraints excluded: chain A residue 271 ILE 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 170 LYS 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 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 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 271 ILE Chi-restraints excluded: chain E residue 18 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.0020 chunk 132 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 146 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 0.9192 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.139926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.093442 restraints weight = 27004.745| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.12 r_work: 0.3324 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1600 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= 0.111 Angle : 0.514 7.331 18745 Z= 0.263 Chirality : 0.040 0.141 2105 Planarity : 0.003 0.032 2285 Dihedral : 14.290 85.340 2415 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.13 % Allowed : 23.27 % Favored : 73.59 % 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: -0.43 (0.21), residues: 1555 helix: 3.28 (0.21), residues: 470 sheet: -1.04 (0.29), residues: 330 loop : -2.42 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS E 277 PHE 0.007 0.001 PHE E 195 TYR 0.015 0.001 TYR D 266 ARG 0.001 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 500) hydrogen bonds : angle 4.04045 ( 1425) covalent geometry : bond 0.00269 (13835) covalent geometry : angle 0.51421 (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 112 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 68 time to evaluate : 2.304 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8531 (tptt) cc_final: 0.7975 (mtmm) REVERT: A 117 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8443 (ttm170) REVERT: A 151 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.6904 (pptt) REVERT: B 64 LYS cc_start: 0.8637 (tptt) cc_final: 0.8281 (mptt) REVERT: B 151 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6670 (pptt) REVERT: C 64 LYS cc_start: 0.8675 (tptt) cc_final: 0.8270 (mptt) REVERT: C 117 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8488 (ttm170) REVERT: C 151 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7140 (pptt) REVERT: D 38 LYS cc_start: 0.8917 (mmtm) cc_final: 0.8565 (mmmt) REVERT: D 64 LYS cc_start: 0.8725 (tptt) cc_final: 0.8328 (mptt) REVERT: D 151 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6884 (pptt) REVERT: D 261 MET cc_start: 0.8536 (ttm) cc_final: 0.8322 (ttp) REVERT: D 312 PHE cc_start: 0.8166 (t80) cc_final: 0.7661 (t80) outliers start: 44 outliers final: 28 residues processed: 109 average time/residue: 0.5540 time to fit residues: 82.5199 Evaluate side-chains 95 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 271 ILE 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 271 ILE Chi-restraints excluded: chain B residue 297 ILE 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 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 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 Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.127466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.087197 restraints weight = 25421.069| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.92 r_work: 0.3210 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13835 Z= 0.252 Angle : 0.603 5.591 18745 Z= 0.312 Chirality : 0.043 0.145 2105 Planarity : 0.004 0.036 2285 Dihedral : 14.695 87.375 2415 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.99 % Allowed : 23.56 % Favored : 73.45 % 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: -0.56 (0.21), residues: 1555 helix: 3.06 (0.21), residues: 470 sheet: -1.20 (0.28), residues: 325 loop : -2.37 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 160 HIS 0.002 0.001 HIS E 235 PHE 0.013 0.001 PHE B 195 TYR 0.014 0.001 TYR C 129 ARG 0.002 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.06035 ( 500) hydrogen bonds : angle 4.50236 ( 1425) covalent geometry : bond 0.00618 (13835) covalent geometry : angle 0.60264 (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 107 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 65 time to evaluate : 2.825 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6790 (pptt) REVERT: A 310 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8999 (mp) REVERT: C 38 LYS cc_start: 0.8886 (mmtm) cc_final: 0.8473 (mmmt) REVERT: C 151 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7238 (pptt) REVERT: D 38 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8548 (mmmt) REVERT: D 151 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.6935 (pptt) REVERT: D 284 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: D 312 PHE cc_start: 0.8210 (t80) cc_final: 0.7740 (t80) outliers start: 42 outliers final: 34 residues processed: 104 average time/residue: 0.5202 time to fit residues: 74.0123 Evaluate side-chains 100 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 61 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 310 LEU 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 169 VAL 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 58 ARG 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 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 76 ILE Chi-restraints excluded: chain D residue 92 ILE 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 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 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: 0.8980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 129 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.139592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.093107 restraints weight = 26706.275| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.11 r_work: 0.3289 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13835 Z= 0.108 Angle : 0.526 7.433 18745 Z= 0.271 Chirality : 0.041 0.173 2105 Planarity : 0.003 0.032 2285 Dihedral : 14.030 87.647 2415 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.21 % Allowed : 24.56 % Favored : 73.24 % 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: 3.26 (0.21), residues: 470 sheet: -1.07 (0.28), residues: 330 loop : -2.41 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 213 HIS 0.003 0.001 HIS B 127 PHE 0.007 0.001 PHE E 37 TYR 0.011 0.001 TYR C 102 ARG 0.001 0.000 ARG D 118 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 500) hydrogen bonds : angle 4.03522 ( 1425) covalent geometry : bond 0.00253 (13835) covalent geometry : angle 0.52624 (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 98 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8413 (mmmt) REVERT: A 64 LYS cc_start: 0.8662 (tptt) cc_final: 0.8374 (mptt) REVERT: A 151 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.6895 (pptt) REVERT: B 64 LYS cc_start: 0.8602 (tptt) cc_final: 0.8291 (mptt) REVERT: B 151 LYS cc_start: 0.7643 (pptt) cc_final: 0.7168 (pptt) REVERT: C 64 LYS cc_start: 0.8651 (tptt) cc_final: 0.8229 (mptt) REVERT: C 151 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7006 (pptt) REVERT: D 38 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8529 (mmmt) REVERT: D 64 LYS cc_start: 0.8693 (tptt) cc_final: 0.8309 (mptt) REVERT: D 151 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6823 (pptt) REVERT: D 261 MET cc_start: 0.8536 (ttm) cc_final: 0.8318 (ttp) REVERT: D 284 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: D 312 PHE cc_start: 0.8175 (t80) cc_final: 0.7664 (t80) outliers start: 31 outliers final: 24 residues processed: 97 average time/residue: 0.3670 time to fit residues: 48.1162 Evaluate side-chains 89 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 169 VAL 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 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 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain E residue 18 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 101 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4163 r_free = 0.4163 target = 0.140429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.094050 restraints weight = 26756.973| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.11 r_work: 0.3304 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1799 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= 0.103 Angle : 0.519 8.638 18745 Z= 0.263 Chirality : 0.040 0.143 2105 Planarity : 0.003 0.031 2285 Dihedral : 13.392 88.985 2415 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.63 % Allowed : 24.13 % Favored : 73.24 % 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: -0.40 (0.21), residues: 1555 helix: 3.30 (0.21), residues: 470 sheet: -0.98 (0.29), residues: 330 loop : -2.42 (0.18), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.002 0.001 HIS B 127 PHE 0.007 0.001 PHE E 195 TYR 0.011 0.001 TYR E 129 ARG 0.001 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 500) hydrogen bonds : angle 3.97172 ( 1425) covalent geometry : bond 0.00242 (13835) covalent geometry : angle 0.51857 (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 102 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 1.663 Fit side-chains REVERT: A 64 LYS cc_start: 0.8533 (tptt) cc_final: 0.8146 (mptt) REVERT: A 151 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6830 (pptt) REVERT: B 64 LYS cc_start: 0.8609 (tptt) cc_final: 0.8271 (mptt) REVERT: B 151 LYS cc_start: 0.7616 (pptt) cc_final: 0.7143 (pptt) REVERT: B 312 PHE cc_start: 0.7927 (t80) cc_final: 0.7665 (t80) REVERT: C 64 LYS cc_start: 0.8657 (tptt) cc_final: 0.8252 (mptt) REVERT: C 151 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7039 (pptt) REVERT: D 38 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8500 (mmmt) REVERT: D 64 LYS cc_start: 0.8687 (tptt) cc_final: 0.8314 (mptt) REVERT: D 151 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6722 (pptt) REVERT: D 261 MET cc_start: 0.8509 (ttm) cc_final: 0.8304 (ttp) REVERT: D 284 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: D 312 PHE cc_start: 0.8169 (t80) cc_final: 0.7657 (t80) outliers start: 37 outliers final: 30 residues processed: 100 average time/residue: 0.3581 time to fit residues: 48.8403 Evaluate side-chains 95 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 58 ARG Chi-restraints excluded: chain B residue 89 VAL 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 169 VAL Chi-restraints excluded: chain B residue 297 ILE 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 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 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 VAL 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 92 ILE 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: 0.1980 chunk 39 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 67 optimal weight: 0.0020 chunk 142 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 150 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4161 r_free = 0.4161 target = 0.140282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.093664 restraints weight = 27118.045| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.13 r_work: 0.3301 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 0.026 13835 Z= 0.110 Angle : 0.517 6.857 18745 Z= 0.265 Chirality : 0.040 0.147 2105 Planarity : 0.003 0.032 2285 Dihedral : 13.092 89.819 2415 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.63 % Allowed : 24.06 % Favored : 73.31 % 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: -0.39 (0.21), residues: 1555 helix: 3.30 (0.21), residues: 470 sheet: -0.97 (0.29), residues: 330 loop : -2.41 (0.18), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 217 HIS 0.002 0.001 HIS D 127 PHE 0.007 0.001 PHE E 195 TYR 0.013 0.001 TYR D 266 ARG 0.001 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 500) hydrogen bonds : angle 3.95202 ( 1425) covalent geometry : bond 0.00263 (13835) covalent geometry : angle 0.51660 (18745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7292.89 seconds wall clock time: 133 minutes 15.69 seconds (7995.69 seconds total)