Starting phenix.real_space_refine on Wed Mar 4 12:07:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i41_35161/03_2026/8i41_35161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i41_35161/03_2026/8i41_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i41_35161/03_2026/8i41_35161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i41_35161/03_2026/8i41_35161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i41_35161/03_2026/8i41_35161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i41_35161/03_2026/8i41_35161.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.03, per 1000 atoms: 0.22 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: 0.95 Conformation dependent library (CDL) restraints added in 595.6 milliseconds 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: 0.32 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: 1.86 Time building geometry restraints manager: 1.28 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: 0.00 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 402 or (resid 403 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 C7B or name C8' 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 O \ 4P or name P )) or (resid 404 and (name CB or name OB or name C' or name C1 or n \ ame 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 C5B or name C6' or name C6 \ B 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 405)) selection = (chain 'C' and (resid 5 through 402 or (resid 403 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 C7B or name C8' 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 O \ 4P or name P )) or (resid 404 and (name CB or name OB or name C' or name C1 or n \ ame 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 C5B or name C6' or name C6 \ B 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 405)) selection = (chain 'D' and (resid 5 through 402 or (resid 403 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 C7B or name C8' 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 O \ 4P or name P )) or (resid 404 and (name CB or name OB or name C' or name C1 or n \ ame 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 C5B or name C6' or name C6 \ B 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 405)) selection = (chain 'E' and (resid 5 through 402 or (resid 403 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 C7B or name C8' 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 O \ 4P or name P )) or (resid 404 and (name CB or name OB or name C' or name C1 or n \ ame 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 C5B or name C6' or name C6 \ B 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 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: 1.250 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.180 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (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 ARG 0.003 0.000 ARG E 58 TYR 0.011 0.001 TYR B 129 PHE 0.006 0.001 PHE E 238 TRP 0.004 0.001 TRP B 47 HIS 0.001 0.000 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00216 (13835) covalent geometry : angle 0.47474 (18745) hydrogen bonds : bond 0.18521 ( 500) hydrogen bonds : angle 5.67340 ( 1425) *********************** 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 : 0.316 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: 0.1652 time to fit residues: 14.5095 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 : 0.504 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7820 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.141596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.095912 restraints weight = 26580.180| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.10 r_work: 0.3328 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13835 Z= 0.112 Angle : 0.519 5.731 18745 Z= 0.266 Chirality : 0.041 0.160 2105 Planarity : 0.004 0.028 2285 Dihedral : 19.715 130.239 2418 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.42 % Allowed : 22.56 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1555 helix: 3.24 (0.21), residues: 470 sheet: -1.68 (0.25), residues: 410 loop : -2.28 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.010 0.001 TYR C 129 PHE 0.011 0.001 PHE A 37 TRP 0.004 0.001 TRP C 217 HIS 0.001 0.000 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00260 (13835) covalent geometry : angle 0.51901 (18745) hydrogen bonds : bond 0.04308 ( 500) hydrogen bonds : angle 4.61448 ( 1425) *********************** 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 83 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8489 (tptt) cc_final: 0.7943 (mtmm) REVERT: B 64 LYS cc_start: 0.8592 (tptt) cc_final: 0.8198 (mptt) REVERT: C 64 LYS cc_start: 0.8630 (tptt) cc_final: 0.8184 (mptt) REVERT: D 64 LYS cc_start: 0.8663 (tptt) cc_final: 0.8239 (mptt) REVERT: D 312 PHE cc_start: 0.8058 (t80) cc_final: 0.7534 (t80) outliers start: 20 outliers final: 9 residues processed: 82 average time/residue: 0.1519 time to fit residues: 17.1740 Evaluate side-chains 69 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 92 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 132 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.137924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.091961 restraints weight = 26889.667| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.08 r_work: 0.3291 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13835 Z= 0.155 Angle : 0.538 5.073 18745 Z= 0.275 Chirality : 0.041 0.148 2105 Planarity : 0.004 0.031 2285 Dihedral : 17.560 108.619 2415 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.71 % Allowed : 22.85 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1555 helix: 3.16 (0.21), residues: 470 sheet: -1.15 (0.29), residues: 330 loop : -2.44 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 109 TYR 0.015 0.001 TYR D 266 PHE 0.012 0.001 PHE D 195 TRP 0.007 0.001 TRP D 160 HIS 0.001 0.000 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00376 (13835) covalent geometry : angle 0.53801 (18745) hydrogen bonds : bond 0.05118 ( 500) hydrogen bonds : angle 4.44610 ( 1425) *********************** 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 89 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.472 Fit side-chains REVERT: A 64 LYS cc_start: 0.8580 (tptt) cc_final: 0.7993 (mtmm) REVERT: B 38 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8380 (mmmt) REVERT: C 64 LYS cc_start: 0.8666 (tptt) cc_final: 0.8221 (mptt) REVERT: D 38 LYS cc_start: 0.8917 (mmtm) cc_final: 0.8543 (mmmt) REVERT: D 64 LYS cc_start: 0.8725 (tptt) cc_final: 0.8276 (mptt) REVERT: D 312 PHE cc_start: 0.8190 (t80) cc_final: 0.7677 (t80) outliers start: 24 outliers final: 14 residues processed: 84 average time/residue: 0.1523 time to fit residues: 17.3723 Evaluate side-chains 77 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 261 MET 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 252 MET Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 141 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 0.0570 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.128293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.088326 restraints weight = 25247.908| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.90 r_work: 0.3229 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1448 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= 0.219 Angle : 0.575 5.283 18745 Z= 0.297 Chirality : 0.042 0.147 2105 Planarity : 0.004 0.034 2285 Dihedral : 16.836 95.399 2415 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.92 % Allowed : 21.99 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1555 helix: 3.08 (0.21), residues: 470 sheet: -1.23 (0.28), residues: 330 loop : -2.50 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 189 TYR 0.022 0.002 TYR D 66 PHE 0.013 0.001 PHE A 195 TRP 0.010 0.001 TRP D 160 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00538 (13835) covalent geometry : angle 0.57457 (18745) hydrogen bonds : bond 0.05741 ( 500) hydrogen bonds : angle 4.55558 ( 1425) *********************** 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 106 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.452 Fit side-chains REVERT: B 64 LYS cc_start: 0.8657 (tptt) cc_final: 0.8288 (mptt) REVERT: C 64 LYS cc_start: 0.8693 (tptt) cc_final: 0.8295 (mptt) REVERT: D 64 LYS cc_start: 0.8752 (tptt) cc_final: 0.8382 (mptt) REVERT: D 312 PHE cc_start: 0.8211 (t80) cc_final: 0.7697 (t80) outliers start: 41 outliers final: 28 residues processed: 99 average time/residue: 0.1449 time to fit residues: 19.7186 Evaluate side-chains 88 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 58 ARG 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 297 ILE Chi-restraints excluded: chain B residue 307 ASN 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 58 ARG Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.125399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084391 restraints weight = 23962.576| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.81 r_work: 0.3112 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13835 Z= 0.229 Angle : 0.590 5.663 18745 Z= 0.305 Chirality : 0.042 0.143 2105 Planarity : 0.004 0.036 2285 Dihedral : 16.159 92.398 2415 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.35 % Allowed : 22.42 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1555 helix: 3.05 (0.21), residues: 470 sheet: -1.28 (0.28), residues: 325 loop : -2.49 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 109 TYR 0.021 0.002 TYR C 66 PHE 0.013 0.001 PHE A 195 TRP 0.009 0.001 TRP D 160 HIS 0.001 0.000 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00565 (13835) covalent geometry : angle 0.59012 (18745) hydrogen bonds : bond 0.05771 ( 500) hydrogen bonds : angle 4.55701 ( 1425) *********************** 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 112 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 65 time to evaluate : 0.476 Fit side-chains REVERT: A 64 LYS cc_start: 0.8630 (tptt) cc_final: 0.8356 (mptt) REVERT: B 124 GLN cc_start: 0.7898 (mp10) cc_final: 0.7626 (mp10) REVERT: D 38 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8602 (mmmt) REVERT: D 117 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8402 (ttm170) REVERT: D 312 PHE cc_start: 0.8206 (t80) cc_final: 0.7717 (t80) REVERT: E 248 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7670 (mppt) outliers start: 47 outliers final: 36 residues processed: 106 average time/residue: 0.1517 time to fit residues: 21.7658 Evaluate side-chains 98 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 92 ILE 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 225 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain 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 117 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 225 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 136 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.128211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087806 restraints weight = 23576.332| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.82 r_work: 0.3173 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1682 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= 0.122 Angle : 0.517 5.233 18745 Z= 0.266 Chirality : 0.040 0.143 2105 Planarity : 0.004 0.032 2285 Dihedral : 15.106 87.642 2415 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.92 % Allowed : 22.49 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.21), residues: 1555 helix: 3.23 (0.21), residues: 470 sheet: -1.25 (0.28), residues: 325 loop : -2.48 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 117 TYR 0.012 0.001 TYR E 129 PHE 0.008 0.001 PHE D 195 TRP 0.004 0.001 TRP B 213 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00295 (13835) covalent geometry : angle 0.51691 (18745) hydrogen bonds : bond 0.04327 ( 500) hydrogen bonds : angle 4.17856 ( 1425) *********************** 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 112 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 71 time to evaluate : 0.482 Fit side-chains REVERT: A 38 LYS cc_start: 0.8822 (mmtm) cc_final: 0.8400 (mmmt) REVERT: A 117 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8348 (ttm170) REVERT: A 151 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6888 (pptt) REVERT: B 64 LYS cc_start: 0.8605 (tptt) cc_final: 0.8288 (mptt) REVERT: B 124 GLN cc_start: 0.7629 (mp10) cc_final: 0.7401 (mp10) REVERT: B 151 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.6707 (pptt) REVERT: C 64 LYS cc_start: 0.8661 (tptt) cc_final: 0.8243 (mptt) REVERT: C 117 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8447 (ttm170) REVERT: C 151 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7106 (pptt) REVERT: D 38 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8562 (mmmt) REVERT: D 64 LYS cc_start: 0.8717 (tptt) cc_final: 0.8376 (mptt) REVERT: D 117 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8427 (ttm170) REVERT: D 151 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.6966 (pptt) REVERT: D 261 MET cc_start: 0.8518 (ttm) cc_final: 0.8277 (ttp) REVERT: D 312 PHE cc_start: 0.8148 (t80) cc_final: 0.7667 (t80) REVERT: E 248 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7630 (mppt) outliers start: 41 outliers final: 21 residues processed: 109 average time/residue: 0.1726 time to fit residues: 24.6332 Evaluate side-chains 92 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 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 151 LYS Chi-restraints excluded: chain B residue 271 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 58 ARG Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 117 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 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 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 40 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.137888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.091277 restraints weight = 26848.916| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.10 r_work: 0.3286 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13835 Z= 0.149 Angle : 0.539 6.621 18745 Z= 0.277 Chirality : 0.041 0.144 2105 Planarity : 0.004 0.033 2285 Dihedral : 14.782 86.116 2415 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.99 % Allowed : 22.70 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1555 helix: 3.19 (0.21), residues: 470 sheet: -1.25 (0.28), residues: 330 loop : -2.47 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 109 TYR 0.013 0.001 TYR A 266 PHE 0.010 0.001 PHE D 195 TRP 0.005 0.001 TRP D 160 HIS 0.001 0.000 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00367 (13835) covalent geometry : angle 0.53930 (18745) hydrogen bonds : bond 0.04729 ( 500) hydrogen bonds : angle 4.25264 ( 1425) *********************** 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 109 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 67 time to evaluate : 0.483 Fit side-chains REVERT: A 38 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8422 (mmmt) REVERT: A 151 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6872 (pptt) REVERT: B 124 GLN cc_start: 0.7704 (mp10) cc_final: 0.7459 (mp10) REVERT: C 38 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8495 (mmmt) REVERT: C 64 LYS cc_start: 0.8668 (tptt) cc_final: 0.8265 (mptt) REVERT: C 117 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8503 (ttm170) REVERT: C 151 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7133 (pptt) REVERT: D 38 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8543 (mmmt) REVERT: D 64 LYS cc_start: 0.8734 (tptt) cc_final: 0.8403 (mptt) REVERT: D 117 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8423 (ttm170) REVERT: D 151 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.6967 (pptt) REVERT: D 261 MET cc_start: 0.8581 (ttm) cc_final: 0.8360 (ttp) REVERT: D 312 PHE cc_start: 0.8188 (t80) cc_final: 0.7731 (t80) REVERT: E 248 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7631 (mppt) outliers start: 42 outliers final: 33 residues processed: 106 average time/residue: 0.1577 time to fit residues: 22.2848 Evaluate side-chains 100 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 135 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 A residue 307 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 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 92 ILE Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4131 r_free = 0.4131 target = 0.137923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.091211 restraints weight = 26748.711| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.11 r_work: 0.3288 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13835 Z= 0.148 Angle : 0.534 5.247 18745 Z= 0.275 Chirality : 0.041 0.141 2105 Planarity : 0.004 0.033 2285 Dihedral : 14.428 84.517 2415 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.27 % Allowed : 22.35 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1555 helix: 3.19 (0.21), residues: 470 sheet: -1.27 (0.27), residues: 330 loop : -2.46 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 109 TYR 0.012 0.001 TYR E 129 PHE 0.010 0.001 PHE D 195 TRP 0.005 0.001 TRP D 160 HIS 0.002 0.000 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00365 (13835) covalent geometry : angle 0.53374 (18745) hydrogen bonds : bond 0.04710 ( 500) hydrogen bonds : angle 4.19594 ( 1425) *********************** 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 110 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 64 time to evaluate : 0.472 Fit side-chains REVERT: A 38 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8447 (mmmt) REVERT: A 64 LYS cc_start: 0.8540 (tptt) cc_final: 0.8199 (mptt) REVERT: A 117 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8318 (ttm170) REVERT: A 151 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.6881 (pptt) REVERT: B 64 LYS cc_start: 0.8574 (tptt) cc_final: 0.8267 (mptt) REVERT: B 124 GLN cc_start: 0.7697 (mp10) cc_final: 0.7461 (mp10) REVERT: C 38 LYS cc_start: 0.8921 (mmtm) cc_final: 0.8536 (mmmt) REVERT: C 64 LYS cc_start: 0.8674 (tptt) cc_final: 0.8273 (mptt) REVERT: C 117 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8481 (ttm170) REVERT: C 151 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7141 (pptt) REVERT: D 38 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8549 (mmmt) REVERT: D 117 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8430 (ttm170) REVERT: D 151 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6923 (pptt) REVERT: D 261 MET cc_start: 0.8576 (ttm) cc_final: 0.8345 (ttp) REVERT: D 284 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: D 312 PHE cc_start: 0.8191 (t80) cc_final: 0.7737 (t80) REVERT: E 248 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7620 (mppt) outliers start: 46 outliers final: 33 residues processed: 109 average time/residue: 0.1594 time to fit residues: 23.2546 Evaluate side-chains 101 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 61 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain 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 92 ILE Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 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 97 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4153 r_free = 0.4153 target = 0.139555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.093284 restraints weight = 27001.063| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.13 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: 0.8361 moved from start: 0.1808 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 : 0.515 6.002 18745 Z= 0.265 Chirality : 0.040 0.141 2105 Planarity : 0.003 0.031 2285 Dihedral : 13.765 84.407 2415 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.70 % Allowed : 22.92 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1555 helix: 3.24 (0.21), residues: 470 sheet: -1.23 (0.27), residues: 330 loop : -2.45 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 109 TYR 0.013 0.001 TYR A 266 PHE 0.009 0.001 PHE B 37 TRP 0.009 0.001 TRP B 47 HIS 0.001 0.000 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00259 (13835) covalent geometry : angle 0.51549 (18745) hydrogen bonds : bond 0.03966 ( 500) hydrogen bonds : angle 3.99271 ( 1425) *********************** 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 106 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8542 (tptt) cc_final: 0.8187 (mptt) REVERT: A 117 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8349 (ttm170) REVERT: A 151 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6896 (pptt) REVERT: B 64 LYS cc_start: 0.8588 (tptt) cc_final: 0.8254 (mptt) REVERT: B 151 LYS cc_start: 0.7769 (pptt) cc_final: 0.7131 (pptt) REVERT: B 312 PHE cc_start: 0.7940 (t80) cc_final: 0.7675 (t80) REVERT: C 38 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8537 (mmmt) REVERT: C 117 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8504 (ttm170) REVERT: C 151 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7065 (pptt) REVERT: D 64 LYS cc_start: 0.8691 (tptt) cc_final: 0.8314 (mptt) REVERT: D 117 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8469 (ttm170) REVERT: D 151 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6815 (pptt) REVERT: D 261 MET cc_start: 0.8508 (ttm) cc_final: 0.8289 (ttp) REVERT: D 284 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7131 (mt0) REVERT: D 312 PHE cc_start: 0.8170 (t80) cc_final: 0.7685 (t80) REVERT: E 248 LYS cc_start: 0.7908 (mmtp) cc_final: 0.7588 (mppt) outliers start: 38 outliers final: 27 residues processed: 105 average time/residue: 0.1712 time to fit residues: 23.6052 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 : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 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 169 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 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 58 ARG Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 96 optimal weight: 4.9990 chunk 47 optimal weight: 0.0020 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 0.0470 chunk 133 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 0.0570 chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4170 r_free = 0.4170 target = 0.140917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094896 restraints weight = 26714.338| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.12 r_work: 0.3350 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1823 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= 0.096 Angle : 0.514 7.022 18745 Z= 0.263 Chirality : 0.040 0.141 2105 Planarity : 0.003 0.031 2285 Dihedral : 13.109 85.337 2415 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.35 % Allowed : 23.77 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1555 helix: 3.28 (0.21), residues: 470 sheet: -1.25 (0.27), residues: 330 loop : -2.44 (0.18), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 109 TYR 0.014 0.001 TYR A 266 PHE 0.007 0.001 PHE A 106 TRP 0.006 0.001 TRP B 47 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00221 (13835) covalent geometry : angle 0.51437 (18745) hydrogen bonds : bond 0.03423 ( 500) hydrogen bonds : angle 3.87754 ( 1425) ********************** 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 98 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8410 (ttm170) REVERT: A 151 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6800 (pptt) REVERT: B 64 LYS cc_start: 0.8609 (tptt) cc_final: 0.8265 (mptt) REVERT: B 151 LYS cc_start: 0.7661 (pptt) cc_final: 0.7036 (pptt) REVERT: B 312 PHE cc_start: 0.7910 (t80) cc_final: 0.7648 (t80) REVERT: C 38 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8520 (mmmt) REVERT: C 117 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8500 (ttm170) REVERT: C 151 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7044 (pptt) REVERT: D 38 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8538 (mmmt) REVERT: D 64 LYS cc_start: 0.8692 (tptt) cc_final: 0.8324 (mptt) REVERT: D 117 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8473 (ttm170) REVERT: D 151 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6797 (pptt) REVERT: D 261 MET cc_start: 0.8491 (ttm) cc_final: 0.8288 (ttp) REVERT: D 284 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.6909 (mt0) REVERT: D 312 PHE cc_start: 0.8147 (t80) cc_final: 0.7637 (t80) outliers start: 33 outliers final: 25 residues processed: 96 average time/residue: 0.1706 time to fit residues: 21.5686 Evaluate side-chains 95 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 169 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 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 58 ARG Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4133 r_free = 0.4133 target = 0.137866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091106 restraints weight = 26812.364| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.11 r_work: 0.3287 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13835 Z= 0.166 Angle : 0.544 6.335 18745 Z= 0.281 Chirality : 0.041 0.141 2105 Planarity : 0.004 0.033 2285 Dihedral : 13.234 87.181 2415 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.56 % Allowed : 23.49 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1555 helix: 3.22 (0.21), residues: 470 sheet: -1.32 (0.27), residues: 330 loop : -2.38 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 109 TYR 0.014 0.001 TYR E 129 PHE 0.010 0.001 PHE D 195 TRP 0.006 0.001 TRP D 160 HIS 0.001 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00412 (13835) covalent geometry : angle 0.54449 (18745) hydrogen bonds : bond 0.04722 ( 500) hydrogen bonds : angle 4.11448 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.03 seconds wall clock time: 49 minutes 1.27 seconds (2941.27 seconds total)