Starting phenix.real_space_refine on Fri Aug 7 00:44:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9snk_55048/08_2026/9snk_55048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9snk_55048/08_2026/9snk_55048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9snk_55048/08_2026/9snk_55048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9snk_55048/08_2026/9snk_55048.map" model { file = "/net/cci-nas-00/data/ceres_data/9snk_55048/08_2026/9snk_55048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9snk_55048/08_2026/9snk_55048.cif" } resolution = 2.59 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= 0.018 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 16 5.49 5 S 28 5.16 5 C 10796 2.51 5 N 2676 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17884 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2979 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 391, 2950 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 374} Conformer: "B" Number of residues, atoms: 391, 2950 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 374} bond proxies already assigned to first conformer: 2968 Chain: "B" Number of atoms: 961 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Conformer: "B" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} bond proxies already assigned to first conformer: 957 Chain: "C" Number of atoms: 2979 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 391, 2950 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 374} Conformer: "B" Number of residues, atoms: 391, 2950 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 374} bond proxies already assigned to first conformer: 2968 Chain: "D" Number of atoms: 961 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Conformer: "B" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} bond proxies already assigned to first conformer: 957 Chain: "F" Number of atoms: 2979 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 391, 2950 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 374} Conformer: "B" Number of residues, atoms: 391, 2950 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 374} bond proxies already assigned to first conformer: 2968 Chain: "G" Number of atoms: 961 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Conformer: "B" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} bond proxies already assigned to first conformer: 957 Chain: "I" Number of atoms: 2979 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 391, 2950 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 374} Conformer: "B" Number of residues, atoms: 391, 2950 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 374} bond proxies already assigned to first conformer: 2968 Chain: "J" Number of atoms: 961 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Conformer: "B" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} bond proxies already assigned to first conformer: 957 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 192 Unusual residues: {'3PE': 1, '6NA': 3, 'FAD': 1, 'GOL': 7, 'LEA': 2, 'SHV': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "B" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 115 Unusual residues: {'3PE': 2, '6NA': 1, 'DKA': 2, 'LEA': 3, 'SHV': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 58 Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 192 Unusual residues: {'3PE': 1, '6NA': 3, 'FAD': 1, 'GOL': 7, 'LEA': 2, 'SHV': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 93 Unusual residues: {'3PE': 1, '6NA': 1, 'DKA': 2, 'LEA': 3, 'SHV': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "F" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 192 Unusual residues: {'3PE': 1, '6NA': 3, 'FAD': 1, 'GOL': 7, 'LEA': 2, 'SHV': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "G" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 93 Unusual residues: {'3PE': 1, '6NA': 1, 'DKA': 2, 'LEA': 3, 'SHV': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "I" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 192 Unusual residues: {'3PE': 1, '6NA': 3, 'FAD': 1, 'GOL': 7, 'LEA': 2, 'SHV': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "J" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 71 Unusual residues: {'6NA': 1, 'DKA': 2, 'LEA': 3, 'SHV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 214 Classifications: {'water': 214} Link IDs: {None: 213} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 214 Classifications: {'water': 214} Link IDs: {None: 213} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "F" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 214 Classifications: {'water': 214} Link IDs: {None: 213} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "I" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 214 Classifications: {'water': 214} Link IDs: {None: 213} Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 7.36, per 1000 atoms: 0.41 Number of scatterers: 17884 At special positions: 0 Unit cell: (139.78, 139.78, 114.26, 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 28 16.00 P 16 15.00 O 4368 8.00 N 2676 7.00 C 10796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3808 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 32 sheets defined 51.9% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.919A pdb=" N LEU A 16 " --> pdb=" O TYR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.615A pdb=" N LEU A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 151 through 154 Processing helix chain 'A' and resid 163 through 184 Proline residue: A 178 - end of helix removed outlier: 3.722A pdb=" N TYR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.862A pdb=" N GLY A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 330 removed outlier: 3.766A pdb=" N TYR A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 384 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 25 through 61 Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 62 through 100 Proline residue: B 79 - end of helix removed outlier: 3.630A pdb=" N ALA B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 116 through 139 Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.919A pdb=" N LEU C 16 " --> pdb=" O TYR C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 removed outlier: 3.615A pdb=" N LEU C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 128 through 150 Processing helix chain 'C' and resid 151 through 154 Processing helix chain 'C' and resid 163 through 184 Proline residue: C 178 - end of helix removed outlier: 3.722A pdb=" N TYR C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 261 through 267 removed outlier: 3.862A pdb=" N GLY C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 330 removed outlier: 3.766A pdb=" N TYR C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 384 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 25 through 61 Proline residue: D 40 - end of helix Processing helix chain 'D' and resid 62 through 100 Proline residue: D 79 - end of helix removed outlier: 3.630A pdb=" N ALA D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 Processing helix chain 'D' and resid 116 through 139 Processing helix chain 'F' and resid 11 through 22 removed outlier: 3.919A pdb=" N LEU F 16 " --> pdb=" O TYR F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 52 removed outlier: 3.615A pdb=" N LEU F 50 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 59 Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 128 through 150 Processing helix chain 'F' and resid 151 through 154 Processing helix chain 'F' and resid 163 through 184 Proline residue: F 178 - end of helix removed outlier: 3.722A pdb=" N TYR F 184 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 207 through 220 Processing helix chain 'F' and resid 261 through 267 removed outlier: 3.862A pdb=" N GLY F 265 " --> pdb=" O ASN F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 330 removed outlier: 3.766A pdb=" N TYR F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE F 326 " --> pdb=" O GLY F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 384 Processing helix chain 'F' and resid 386 through 392 Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 25 through 61 Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 62 through 100 Proline residue: G 79 - end of helix removed outlier: 3.630A pdb=" N ALA G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 Processing helix chain 'G' and resid 116 through 139 Processing helix chain 'I' and resid 11 through 22 removed outlier: 3.919A pdb=" N LEU I 16 " --> pdb=" O TYR I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 52 removed outlier: 3.615A pdb=" N LEU I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 59 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 128 through 150 Processing helix chain 'I' and resid 151 through 154 Processing helix chain 'I' and resid 163 through 184 Proline residue: I 178 - end of helix removed outlier: 3.722A pdb=" N TYR I 184 " --> pdb=" O LEU I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 191 Processing helix chain 'I' and resid 207 through 220 Processing helix chain 'I' and resid 261 through 267 removed outlier: 3.862A pdb=" N GLY I 265 " --> pdb=" O ASN I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 330 removed outlier: 3.766A pdb=" N TYR I 323 " --> pdb=" O GLU I 319 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE I 326 " --> pdb=" O GLY I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 384 Processing helix chain 'I' and resid 386 through 392 Processing helix chain 'J' and resid 19 through 24 Processing helix chain 'J' and resid 25 through 61 Proline residue: J 40 - end of helix Processing helix chain 'J' and resid 62 through 100 Proline residue: J 79 - end of helix removed outlier: 3.630A pdb=" N ALA J 100 " --> pdb=" O ASP J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 116 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77 removed outlier: 8.529A pdb=" N ASP A 74 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 32 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LYS A 76 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 34 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 103 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 112 removed outlier: 4.156A pdb=" N GLY A 257 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.749A pdb=" N LEU A 193 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU A 226 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 195 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 251 " --> pdb=" O THR A 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.562A pdb=" N ASN A 233 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.301A pdb=" N ALA A 276 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 77 removed outlier: 8.529A pdb=" N ASP C 74 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 32 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LYS C 76 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 34 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 103 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AB2, first strand: chain 'C' and resid 80 through 84 Processing sheet with id=AB3, first strand: chain 'C' and resid 109 through 112 removed outlier: 4.156A pdb=" N GLY C 257 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 223 through 227 removed outlier: 6.749A pdb=" N LEU C 193 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU C 226 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 195 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 251 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.562A pdb=" N ASN C 233 " --> pdb=" O ASP C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 272 removed outlier: 6.301A pdb=" N ALA C 276 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 343 through 347 Processing sheet with id=AB8, first strand: chain 'F' and resid 73 through 77 removed outlier: 8.529A pdb=" N ASP F 74 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL F 32 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LYS F 76 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 34 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU F 103 " --> pdb=" O PHE F 291 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 40 through 42 Processing sheet with id=AC1, first strand: chain 'F' and resid 80 through 84 Processing sheet with id=AC2, first strand: chain 'F' and resid 109 through 112 removed outlier: 4.156A pdb=" N GLY F 257 " --> pdb=" O ALA F 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 223 through 227 removed outlier: 6.749A pdb=" N LEU F 193 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU F 226 " --> pdb=" O LEU F 193 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU F 195 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR F 251 " --> pdb=" O THR F 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.562A pdb=" N ASN F 233 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 271 through 272 removed outlier: 6.301A pdb=" N ALA F 276 " --> pdb=" O VAL F 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 343 through 347 Processing sheet with id=AC7, first strand: chain 'I' and resid 73 through 77 removed outlier: 8.529A pdb=" N ASP I 74 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL I 32 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LYS I 76 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL I 34 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU I 103 " --> pdb=" O PHE I 291 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 40 through 42 Processing sheet with id=AC9, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AD1, first strand: chain 'I' and resid 109 through 112 removed outlier: 4.156A pdb=" N GLY I 257 " --> pdb=" O ALA I 112 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 223 through 227 removed outlier: 6.749A pdb=" N LEU I 193 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU I 226 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU I 195 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR I 251 " --> pdb=" O THR I 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 231 through 235 removed outlier: 3.562A pdb=" N ASN I 233 " --> pdb=" O ASP I 240 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 271 through 272 removed outlier: 6.301A pdb=" N ALA I 276 " --> pdb=" O VAL I 298 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 343 through 347 896 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3104 1.33 - 1.45: 3768 1.45 - 1.57: 10128 1.57 - 1.69: 32 1.69 - 1.81: 56 Bond restraints: 17088 Sorted by residual: bond pdb=" N GLU D 86 " pdb=" CA GLU D 86 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.28e-02 6.10e+03 5.00e+00 bond pdb=" N GLU J 86 " pdb=" CA GLU J 86 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.28e-02 6.10e+03 5.00e+00 bond pdb=" N GLU B 86 " pdb=" CA GLU B 86 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.28e-02 6.10e+03 5.00e+00 bond pdb=" N GLU G 86 " pdb=" CA GLU G 86 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.28e-02 6.10e+03 5.00e+00 bond pdb=" N ASP D 68 " pdb=" CA ASP D 68 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.21e-02 6.83e+03 4.27e+00 ... (remaining 17083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 22556 1.53 - 3.05: 296 3.05 - 4.58: 76 4.58 - 6.11: 36 6.11 - 7.63: 8 Bond angle restraints: 22972 Sorted by residual: angle pdb=" CA ASP D 68 " pdb=" C ASP D 68 " pdb=" O ASP D 68 " ideal model delta sigma weight residual 120.55 116.45 4.10 1.06e+00 8.90e-01 1.50e+01 angle pdb=" CA ASP G 68 " pdb=" C ASP G 68 " pdb=" O ASP G 68 " ideal model delta sigma weight residual 120.55 116.45 4.10 1.06e+00 8.90e-01 1.50e+01 angle pdb=" CA ASP B 68 " pdb=" C ASP B 68 " pdb=" O ASP B 68 " ideal model delta sigma weight residual 120.55 116.45 4.10 1.06e+00 8.90e-01 1.50e+01 angle pdb=" CA ASP J 68 " pdb=" C ASP J 68 " pdb=" O ASP J 68 " ideal model delta sigma weight residual 120.55 116.45 4.10 1.06e+00 8.90e-01 1.50e+01 angle pdb=" N ARG A 22 " pdb=" CA ARG A 22 " pdb=" C ARG A 22 " ideal model delta sigma weight residual 113.18 108.75 4.43 1.21e+00 6.83e-01 1.34e+01 ... (remaining 22967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 9700 23.62 - 47.25: 684 47.25 - 70.87: 120 70.87 - 94.50: 20 94.50 - 118.12: 8 Dihedral angle restraints: 10532 sinusoidal: 4572 harmonic: 5960 Sorted by residual: dihedral pdb=" O21 3PE I 407 " pdb=" C2 3PE I 407 " pdb=" C3 3PE I 407 " pdb=" O31 3PE I 407 " ideal model delta sinusoidal sigma weight residual 60.47 -57.65 118.12 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" O21 3PE A 407 " pdb=" C2 3PE A 407 " pdb=" C3 3PE A 407 " pdb=" O31 3PE A 407 " ideal model delta sinusoidal sigma weight residual 60.47 -57.65 118.12 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" O21 3PE C 407 " pdb=" C2 3PE C 407 " pdb=" C3 3PE C 407 " pdb=" O31 3PE C 407 " ideal model delta sinusoidal sigma weight residual 60.47 -57.65 118.12 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 10529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2084 0.050 - 0.100: 408 0.100 - 0.150: 112 0.150 - 0.200: 4 0.200 - 0.250: 8 Chirality restraints: 2616 Sorted by residual: chirality pdb=" C2 3PE B 205 " pdb=" C1 3PE B 205 " pdb=" C3 3PE B 205 " pdb=" O21 3PE B 205 " both_signs ideal model delta sigma weight residual False -2.53 -2.28 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C2 3PE D 205 " pdb=" C1 3PE D 205 " pdb=" C3 3PE D 205 " pdb=" O21 3PE D 205 " both_signs ideal model delta sigma weight residual False -2.53 -2.28 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C2 3PE G 205 " pdb=" C1 3PE G 205 " pdb=" C3 3PE G 205 " pdb=" O21 3PE G 205 " both_signs ideal model delta sigma weight residual False -2.53 -2.28 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2613 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 116 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO B 117 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 117 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 117 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 116 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO J 117 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO J 117 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 117 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 116 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO D 117 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 117 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 117 " 0.019 5.00e-02 4.00e+02 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2800 2.76 - 3.29: 15760 3.29 - 3.83: 31343 3.83 - 4.36: 41621 4.36 - 4.90: 66960 Nonbonded interactions: 158484 Sorted by model distance: nonbonded pdb=" OG1 THR A 111 " pdb=" O2 GOL A 410 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C 111 " pdb=" O2 GOL C 410 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR F 111 " pdb=" O2 GOL F 410 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR I 111 " pdb=" O2 GOL I 410 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP I 240 " pdb=" O HOH I 501 " model vdw 2.226 3.040 ... (remaining 158479 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 2 or resid 4 through 72 or resid 74 through 87 or resid 89 \ through 133 or resid 135 through 136 or resid 138 through 417)) selection = (chain 'C' and (resid 2 or resid 4 through 72 or resid 74 through 87 or resid 89 \ through 133 or resid 135 through 136 or resid 138 through 417)) selection = (chain 'F' and (resid 2 or resid 4 through 72 or resid 74 through 87 or resid 89 \ through 133 or resid 135 through 136 or resid 138 through 417)) selection = (chain 'I' and (resid 2 or resid 4 through 72 or resid 74 through 87 or resid 89 \ through 133 or resid 135 through 136 or resid 138 through 417)) } ncs_group { reference = (chain 'B' and (resid 18 through 56 or resid 58 through 139 or resid 206 through \ 208)) selection = (chain 'D' and (resid 18 through 56 or resid 58 through 139 or resid 206 through \ 208)) selection = (chain 'G' and (resid 18 through 56 or resid 58 through 139 or resid 206 through \ 208)) selection = (chain 'J' and (resid 18 through 56 or resid 58 through 139 or resid 206 through \ 208)) } 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=0.06 max=1.00 mean=0.99 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: 12.420 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: 0.640 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.990 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 : 0.003 0.029 17088 Z= 0.138 Angle : 0.532 7.634 22972 Z= 0.288 Chirality : 0.044 0.250 2616 Planarity : 0.004 0.050 2884 Dihedral : 16.728 118.121 6724 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.70 % Allowed : 15.65 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 2060 helix: 2.28 (0.17), residues: 1008 sheet: 0.85 (0.33), residues: 280 loop : 0.18 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.016 0.001 TYR F 380 PHE 0.010 0.001 PHE F 83 TRP 0.016 0.002 TRP I 315 HIS 0.003 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (17088) covalent geometry : angle 0.53239 / 0.29 (22972) hydrogen bonds : bond 0.12847 / 8.13 ( 896) hydrogen bonds : angle 4.84876 / 3.30 ( 2520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 0.618 Fit side-chains REVERT: A 28 GLU cc_start: 0.8331 (mp0) cc_final: 0.7947 (mp0) REVERT: A 69 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7761 (ttmm) REVERT: A 87 LYS cc_start: 0.8232 (mttt) cc_final: 0.7961 (mtmt) REVERT: A 220 LYS cc_start: 0.8375 (tttt) cc_final: 0.7625 (ttpt) REVERT: B 82 GLU cc_start: 0.8224 (tt0) cc_final: 0.7602 (mm-30) REVERT: B 86 GLU cc_start: 0.8812 (tp30) cc_final: 0.8594 (tp30) REVERT: B 115 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8050 (mtpp) REVERT: C 28 GLU cc_start: 0.8332 (mp0) cc_final: 0.7945 (mp0) REVERT: C 69 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7764 (ttmm) REVERT: C 87 LYS cc_start: 0.8233 (mttt) cc_final: 0.7961 (mtmt) REVERT: C 220 LYS cc_start: 0.8374 (tttt) cc_final: 0.7625 (ttpt) REVERT: D 82 GLU cc_start: 0.8226 (tt0) cc_final: 0.7602 (mm-30) REVERT: D 86 GLU cc_start: 0.8811 (tp30) cc_final: 0.8594 (tp30) REVERT: D 115 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8053 (mtpp) REVERT: F 28 GLU cc_start: 0.8334 (mp0) cc_final: 0.7945 (mp0) REVERT: F 69 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7763 (ttmm) REVERT: F 87 LYS cc_start: 0.8233 (mttt) cc_final: 0.7963 (mtmt) REVERT: F 220 LYS cc_start: 0.8374 (tttt) cc_final: 0.7624 (ttpt) REVERT: G 82 GLU cc_start: 0.8224 (tt0) cc_final: 0.7601 (mm-30) REVERT: G 86 GLU cc_start: 0.8813 (tp30) cc_final: 0.8594 (tp30) REVERT: G 115 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8052 (mtpp) REVERT: I 28 GLU cc_start: 0.8333 (mp0) cc_final: 0.7946 (mp0) REVERT: I 69 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7749 (ttmm) REVERT: I 87 LYS cc_start: 0.8234 (mttt) cc_final: 0.7946 (mtmt) REVERT: I 220 LYS cc_start: 0.8370 (tttt) cc_final: 0.7622 (ttpt) REVERT: J 82 GLU cc_start: 0.8226 (tt0) cc_final: 0.7602 (mm-30) REVERT: J 86 GLU cc_start: 0.8813 (tp30) cc_final: 0.8594 (tp30) REVERT: J 115 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8051 (mtpp) outliers start: 12 outliers final: 8 residues processed: 244 average time/residue: 0.6780 time to fit residues: 182.4172 Evaluate side-chains 236 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 170 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113782 restraints weight = 74438.222| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.58 r_work: 0.3236 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17088 Z= 0.098 Angle : 0.414 4.724 22972 Z= 0.222 Chirality : 0.041 0.129 2616 Planarity : 0.004 0.033 2884 Dihedral : 10.888 103.405 2964 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.64 % Allowed : 15.42 % Favored : 82.94 % 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: 2.18 (0.19), residues: 2060 helix: 2.52 (0.17), residues: 1016 sheet: 1.29 (0.35), residues: 252 loop : 0.11 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 142 TYR 0.009 0.001 TYR I 380 PHE 0.011 0.001 PHE A 83 TRP 0.015 0.002 TRP F 315 HIS 0.002 0.001 HIS I 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (17088) covalent geometry : angle 0.41405 / 0.22 (22972) hydrogen bonds : bond 0.03868 / 2.55 ( 896) hydrogen bonds : angle 4.03788 / 2.75 ( 2520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.735 Fit side-chains REVERT: A 28 GLU cc_start: 0.8423 (mp0) cc_final: 0.8101 (mp0) REVERT: A 69 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7864 (ttmm) REVERT: A 87 LYS cc_start: 0.8390 (mttt) cc_final: 0.8142 (mtmt) REVERT: A 220 LYS cc_start: 0.8389 (tttt) cc_final: 0.7748 (ttpt) REVERT: B 82 GLU cc_start: 0.7852 (tt0) cc_final: 0.7302 (mm-30) REVERT: B 86 GLU cc_start: 0.8123 (tp30) cc_final: 0.7775 (tp30) REVERT: B 105 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8278 (mp) REVERT: B 115 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7724 (mtpp) REVERT: C 28 GLU cc_start: 0.8430 (mp0) cc_final: 0.8106 (mp0) REVERT: C 69 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7867 (ttmm) REVERT: C 87 LYS cc_start: 0.8384 (mttt) cc_final: 0.8136 (mtmt) REVERT: C 220 LYS cc_start: 0.8389 (tttt) cc_final: 0.7749 (ttpt) REVERT: D 82 GLU cc_start: 0.7853 (tt0) cc_final: 0.7302 (mm-30) REVERT: D 86 GLU cc_start: 0.8122 (tp30) cc_final: 0.7773 (tp30) REVERT: D 105 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8275 (mp) REVERT: D 115 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7722 (mtpp) REVERT: F 28 GLU cc_start: 0.8429 (mp0) cc_final: 0.8105 (mp0) REVERT: F 69 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7870 (ttmm) REVERT: F 87 LYS cc_start: 0.8385 (mttt) cc_final: 0.8136 (mtmt) REVERT: F 220 LYS cc_start: 0.8387 (tttt) cc_final: 0.7751 (ttpt) REVERT: G 82 GLU cc_start: 0.7854 (tt0) cc_final: 0.7299 (mm-30) REVERT: G 86 GLU cc_start: 0.8126 (tp30) cc_final: 0.7776 (tp30) REVERT: G 105 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8281 (mp) REVERT: G 115 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7720 (mtpp) REVERT: I 28 GLU cc_start: 0.8429 (mp0) cc_final: 0.8105 (mp0) REVERT: I 69 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7868 (ttmm) REVERT: I 87 LYS cc_start: 0.8381 (mttt) cc_final: 0.8112 (mtmt) REVERT: I 220 LYS cc_start: 0.8392 (tttt) cc_final: 0.7750 (ttpt) REVERT: J 82 GLU cc_start: 0.7853 (tt0) cc_final: 0.7296 (mm-30) REVERT: J 86 GLU cc_start: 0.8127 (tp30) cc_final: 0.7778 (tp30) REVERT: J 105 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8278 (mp) REVERT: J 115 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7718 (mtpp) outliers start: 28 outliers final: 8 residues processed: 256 average time/residue: 0.6805 time to fit residues: 193.5576 Evaluate side-chains 224 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 6 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 HIS C 383 HIS F 383 HIS I 383 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110298 restraints weight = 66512.847| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.92 r_work: 0.3161 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 17088 Z= 0.240 Angle : 0.579 5.990 22972 Z= 0.301 Chirality : 0.049 0.146 2616 Planarity : 0.004 0.039 2884 Dihedral : 11.734 107.264 2960 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.57 % Allowed : 14.72 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.19), residues: 2060 helix: 2.10 (0.17), residues: 1016 sheet: 1.02 (0.33), residues: 252 loop : -0.06 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 142 TYR 0.013 0.002 TYR I 323 PHE 0.016 0.002 PHE A 83 TRP 0.015 0.003 TRP A 315 HIS 0.005 0.001 HIS I 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 (17088) covalent geometry : angle 0.57854 / 0.30 (22972) hydrogen bonds : bond 0.06182 / 4.11 ( 896) hydrogen bonds : angle 4.25149 / 2.91 ( 2520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.696 Fit side-chains REVERT: A 28 GLU cc_start: 0.8490 (mp0) cc_final: 0.8180 (mp0) REVERT: A 87 LYS cc_start: 0.8557 (mttt) cc_final: 0.8295 (mttt) REVERT: A 197 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: A 220 LYS cc_start: 0.8497 (tttt) cc_final: 0.7950 (ttpt) REVERT: B 82 GLU cc_start: 0.8049 (tt0) cc_final: 0.7607 (mm-30) REVERT: B 86 GLU cc_start: 0.8305 (tp30) cc_final: 0.7986 (tp30) REVERT: B 115 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8032 (mtpp) REVERT: C 28 GLU cc_start: 0.8490 (mp0) cc_final: 0.8181 (mp0) REVERT: C 87 LYS cc_start: 0.8545 (mttt) cc_final: 0.8283 (mttt) REVERT: C 197 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: C 220 LYS cc_start: 0.8498 (tttt) cc_final: 0.7957 (ttpt) REVERT: D 82 GLU cc_start: 0.8051 (tt0) cc_final: 0.7606 (mm-30) REVERT: D 86 GLU cc_start: 0.8310 (tp30) cc_final: 0.7992 (tp30) REVERT: D 115 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8037 (mtpp) REVERT: F 28 GLU cc_start: 0.8481 (mp0) cc_final: 0.8172 (mp0) REVERT: F 87 LYS cc_start: 0.8548 (mttt) cc_final: 0.8286 (mttt) REVERT: F 197 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: F 220 LYS cc_start: 0.8498 (tttt) cc_final: 0.7954 (ttpt) REVERT: G 82 GLU cc_start: 0.8051 (tt0) cc_final: 0.7604 (mm-30) REVERT: G 86 GLU cc_start: 0.8312 (tp30) cc_final: 0.7996 (tp30) REVERT: G 115 LYS cc_start: 0.8376 (mtpt) cc_final: 0.8033 (mtpp) REVERT: I 28 GLU cc_start: 0.8489 (mp0) cc_final: 0.8179 (mp0) REVERT: I 87 LYS cc_start: 0.8552 (mttt) cc_final: 0.8288 (mttt) REVERT: I 197 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7768 (tp30) REVERT: I 220 LYS cc_start: 0.8499 (tttt) cc_final: 0.7952 (ttpt) REVERT: J 82 GLU cc_start: 0.8044 (tt0) cc_final: 0.7596 (mm-30) REVERT: J 86 GLU cc_start: 0.8305 (tp30) cc_final: 0.7985 (tp30) REVERT: J 115 LYS cc_start: 0.8374 (mtpt) cc_final: 0.8033 (mtpp) outliers start: 44 outliers final: 20 residues processed: 252 average time/residue: 0.7112 time to fit residues: 198.5338 Evaluate side-chains 232 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 76 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN D 127 ASN G 127 ASN J 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113869 restraints weight = 79661.596| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.30 r_work: 0.3193 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17088 Z= 0.116 Angle : 0.435 4.758 22972 Z= 0.233 Chirality : 0.042 0.132 2616 Planarity : 0.004 0.036 2884 Dihedral : 11.180 102.423 2960 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.40 % Allowed : 16.12 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.19), residues: 2060 helix: 2.30 (0.17), residues: 1016 sheet: 0.94 (0.34), residues: 256 loop : -0.02 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 221 TYR 0.011 0.001 TYR A 380 PHE 0.012 0.001 PHE A 83 TRP 0.016 0.002 TRP C 315 HIS 0.003 0.001 HIS I 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (17088) covalent geometry : angle 0.43505 / 0.23 (22972) hydrogen bonds : bond 0.04303 / 2.86 ( 896) hydrogen bonds : angle 4.00382 / 2.73 ( 2520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.727 Fit side-chains REVERT: A 28 GLU cc_start: 0.8503 (mp0) cc_final: 0.8177 (mp0) REVERT: A 87 LYS cc_start: 0.8505 (mttt) cc_final: 0.8254 (mtmt) REVERT: A 192 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8721 (mmtt) REVERT: A 197 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: A 220 LYS cc_start: 0.8468 (tttt) cc_final: 0.7924 (ttpt) REVERT: B 82 GLU cc_start: 0.8015 (tt0) cc_final: 0.7566 (mm-30) REVERT: B 86 GLU cc_start: 0.8216 (tp30) cc_final: 0.7913 (tp30) REVERT: B 105 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8370 (mp) REVERT: B 115 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7975 (mtpp) REVERT: C 28 GLU cc_start: 0.8507 (mp0) cc_final: 0.8179 (mp0) REVERT: C 87 LYS cc_start: 0.8497 (mttt) cc_final: 0.8247 (mtmt) REVERT: C 192 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8716 (mmtt) REVERT: C 197 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: C 220 LYS cc_start: 0.8470 (tttt) cc_final: 0.7932 (ttpt) REVERT: D 82 GLU cc_start: 0.8013 (tt0) cc_final: 0.7554 (mm-30) REVERT: D 86 GLU cc_start: 0.8217 (tp30) cc_final: 0.7914 (tp30) REVERT: D 105 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8368 (mp) REVERT: D 115 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7976 (mtpp) REVERT: F 28 GLU cc_start: 0.8504 (mp0) cc_final: 0.8178 (mp0) REVERT: F 87 LYS cc_start: 0.8500 (mttt) cc_final: 0.8250 (mtmt) REVERT: F 192 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8716 (mmtt) REVERT: F 197 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: F 220 LYS cc_start: 0.8476 (tttt) cc_final: 0.7934 (ttpt) REVERT: G 82 GLU cc_start: 0.8021 (tt0) cc_final: 0.7567 (mm-30) REVERT: G 86 GLU cc_start: 0.8228 (tp30) cc_final: 0.7926 (tp30) REVERT: G 105 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8373 (mp) REVERT: G 115 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7974 (mtpp) REVERT: I 28 GLU cc_start: 0.8504 (mp0) cc_final: 0.8176 (mp0) REVERT: I 87 LYS cc_start: 0.8508 (mttt) cc_final: 0.8258 (mtmt) REVERT: I 192 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8720 (mmtt) REVERT: I 197 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: I 220 LYS cc_start: 0.8470 (tttt) cc_final: 0.7929 (ttpt) REVERT: J 82 GLU cc_start: 0.8019 (tt0) cc_final: 0.7560 (mm-30) REVERT: J 86 GLU cc_start: 0.8223 (tp30) cc_final: 0.7919 (tp30) REVERT: J 105 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8371 (mp) REVERT: J 115 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7974 (mtpp) outliers start: 24 outliers final: 12 residues processed: 236 average time/residue: 0.7095 time to fit residues: 185.3958 Evaluate side-chains 228 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain I residue 296 SER Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 152 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0770 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN D 127 ASN G 127 ASN J 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111745 restraints weight = 70171.619| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.08 r_work: 0.3157 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17088 Z= 0.150 Angle : 0.474 4.784 22972 Z= 0.251 Chirality : 0.044 0.135 2616 Planarity : 0.004 0.037 2884 Dihedral : 11.172 99.756 2960 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.10 % Allowed : 15.42 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 2060 helix: 2.26 (0.17), residues: 1020 sheet: 0.89 (0.34), residues: 256 loop : -0.07 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 221 TYR 0.012 0.002 TYR C 380 PHE 0.014 0.002 PHE A 83 TRP 0.016 0.003 TRP I 315 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (17088) covalent geometry : angle 0.47409 / 0.25 (22972) hydrogen bonds : bond 0.04876 / 3.25 ( 896) hydrogen bonds : angle 4.03562 / 2.76 ( 2520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.615 Fit side-chains REVERT: A 28 GLU cc_start: 0.8483 (mp0) cc_final: 0.8147 (mp0) REVERT: A 87 LYS cc_start: 0.8541 (mttt) cc_final: 0.8277 (mtmt) REVERT: A 192 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8700 (mmtt) REVERT: A 197 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7721 (tp30) REVERT: A 220 LYS cc_start: 0.8495 (tttt) cc_final: 0.7916 (ttpt) REVERT: B 82 GLU cc_start: 0.8071 (tt0) cc_final: 0.7590 (mm-30) REVERT: B 86 GLU cc_start: 0.8297 (tp30) cc_final: 0.7998 (tp30) REVERT: B 105 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8347 (mp) REVERT: B 115 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8010 (mtpp) REVERT: C 28 GLU cc_start: 0.8483 (mp0) cc_final: 0.8147 (mp0) REVERT: C 87 LYS cc_start: 0.8533 (mttt) cc_final: 0.8267 (mtmt) REVERT: C 192 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8698 (mmtt) REVERT: C 197 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: C 220 LYS cc_start: 0.8495 (tttt) cc_final: 0.7922 (ttpt) REVERT: D 82 GLU cc_start: 0.8062 (tt0) cc_final: 0.7578 (mm-30) REVERT: D 86 GLU cc_start: 0.8296 (tp30) cc_final: 0.8000 (tp30) REVERT: D 105 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8348 (mp) REVERT: D 115 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8008 (mtpp) REVERT: F 28 GLU cc_start: 0.8484 (mp0) cc_final: 0.8149 (mp0) REVERT: F 87 LYS cc_start: 0.8533 (mttt) cc_final: 0.8269 (mtmt) REVERT: F 192 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8701 (mmtt) REVERT: F 197 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: F 220 LYS cc_start: 0.8504 (tttt) cc_final: 0.7932 (ttpt) REVERT: G 82 GLU cc_start: 0.8071 (tt0) cc_final: 0.7587 (mm-30) REVERT: G 86 GLU cc_start: 0.8297 (tp30) cc_final: 0.7999 (tp30) REVERT: G 105 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8348 (mp) REVERT: G 115 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8012 (mtpp) REVERT: I 28 GLU cc_start: 0.8484 (mp0) cc_final: 0.8146 (mp0) REVERT: I 87 LYS cc_start: 0.8535 (mttt) cc_final: 0.8268 (mtmt) REVERT: I 192 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8703 (mmtt) REVERT: I 197 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7722 (tp30) REVERT: I 220 LYS cc_start: 0.8501 (tttt) cc_final: 0.7926 (ttpt) REVERT: J 82 GLU cc_start: 0.8068 (tt0) cc_final: 0.7584 (mm-30) REVERT: J 86 GLU cc_start: 0.8299 (tp30) cc_final: 0.7999 (tp30) REVERT: J 105 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8354 (mp) REVERT: J 115 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8006 (mtpp) outliers start: 36 outliers final: 12 residues processed: 236 average time/residue: 0.6926 time to fit residues: 181.0517 Evaluate side-chains 224 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain I residue 296 SER Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 153 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115391 restraints weight = 73474.018| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.12 r_work: 0.3206 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17088 Z= 0.108 Angle : 0.425 4.760 22972 Z= 0.228 Chirality : 0.042 0.129 2616 Planarity : 0.004 0.036 2884 Dihedral : 10.880 94.463 2960 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.10 % Allowed : 16.12 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.19), residues: 2060 helix: 2.45 (0.17), residues: 1016 sheet: 0.98 (0.34), residues: 256 loop : -0.01 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 221 TYR 0.011 0.001 TYR A 380 PHE 0.012 0.001 PHE I 83 TRP 0.017 0.002 TRP I 315 HIS 0.003 0.001 HIS I 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (17088) covalent geometry : angle 0.42454 / 0.23 (22972) hydrogen bonds : bond 0.04080 / 2.72 ( 896) hydrogen bonds : angle 3.91606 / 2.68 ( 2520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.677 Fit side-chains REVERT: A 28 GLU cc_start: 0.8493 (mp0) cc_final: 0.8171 (mp0) REVERT: A 76 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7737 (tmtm) REVERT: A 87 LYS cc_start: 0.8519 (mttt) cc_final: 0.8262 (mtmt) REVERT: A 192 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8694 (mmtt) REVERT: A 220 LYS cc_start: 0.8490 (tttt) cc_final: 0.7911 (ttpt) REVERT: B 82 GLU cc_start: 0.8057 (tt0) cc_final: 0.7577 (mm-30) REVERT: B 86 GLU cc_start: 0.8252 (tp30) cc_final: 0.7941 (tp30) REVERT: B 105 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8376 (mp) REVERT: B 115 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7949 (mtpp) REVERT: C 28 GLU cc_start: 0.8497 (mp0) cc_final: 0.8177 (mp0) REVERT: C 76 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7736 (tmtm) REVERT: C 87 LYS cc_start: 0.8522 (mttt) cc_final: 0.8266 (mtmt) REVERT: C 192 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8689 (mmtt) REVERT: C 220 LYS cc_start: 0.8488 (tttt) cc_final: 0.7909 (ttpt) REVERT: D 82 GLU cc_start: 0.8046 (tt0) cc_final: 0.7566 (mm-30) REVERT: D 86 GLU cc_start: 0.8253 (tp30) cc_final: 0.7944 (tp30) REVERT: D 105 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8371 (mp) REVERT: D 115 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7955 (mtpp) REVERT: F 28 GLU cc_start: 0.8489 (mp0) cc_final: 0.8169 (mp0) REVERT: F 76 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7735 (tmtm) REVERT: F 87 LYS cc_start: 0.8520 (mttt) cc_final: 0.8266 (mtmt) REVERT: F 192 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8693 (mmtt) REVERT: F 220 LYS cc_start: 0.8486 (tttt) cc_final: 0.7902 (ttpt) REVERT: G 82 GLU cc_start: 0.8041 (tt0) cc_final: 0.7566 (mm-30) REVERT: G 86 GLU cc_start: 0.8254 (tp30) cc_final: 0.7945 (tp30) REVERT: G 105 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8377 (mp) REVERT: G 115 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7952 (mtpp) REVERT: I 28 GLU cc_start: 0.8490 (mp0) cc_final: 0.8167 (mp0) REVERT: I 76 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7736 (tmtm) REVERT: I 87 LYS cc_start: 0.8519 (mttt) cc_final: 0.8262 (mtmt) REVERT: I 192 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8700 (mmtt) REVERT: I 220 LYS cc_start: 0.8491 (tttt) cc_final: 0.7907 (ttpt) REVERT: J 82 GLU cc_start: 0.8054 (tt0) cc_final: 0.7571 (mm-30) REVERT: J 86 GLU cc_start: 0.8256 (tp30) cc_final: 0.7945 (tp30) REVERT: J 105 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8377 (mp) REVERT: J 115 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7950 (mtpp) outliers start: 36 outliers final: 20 residues processed: 256 average time/residue: 0.6325 time to fit residues: 180.5398 Evaluate side-chains 244 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 296 SER Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 104 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 187 optimal weight: 0.0040 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114239 restraints weight = 73307.075| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.08 r_work: 0.3201 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17088 Z= 0.134 Angle : 0.457 4.782 22972 Z= 0.243 Chirality : 0.043 0.134 2616 Planarity : 0.004 0.037 2884 Dihedral : 10.905 92.268 2960 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.34 % Allowed : 16.18 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 2060 helix: 2.37 (0.17), residues: 1020 sheet: 0.94 (0.34), residues: 256 loop : -0.03 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 221 TYR 0.012 0.001 TYR A 380 PHE 0.013 0.001 PHE F 83 TRP 0.017 0.003 TRP I 315 HIS 0.004 0.001 HIS I 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (17088) covalent geometry : angle 0.45732 / 0.24 (22972) hydrogen bonds : bond 0.04588 / 3.06 ( 896) hydrogen bonds : angle 3.96778 / 2.71 ( 2520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.680 Fit side-chains REVERT: A 28 GLU cc_start: 0.8483 (mp0) cc_final: 0.8164 (mp0) REVERT: A 76 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7758 (tmtm) REVERT: A 87 LYS cc_start: 0.8554 (mttt) cc_final: 0.8299 (mtmt) REVERT: A 148 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7691 (mttt) REVERT: A 192 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8696 (mmtt) REVERT: A 220 LYS cc_start: 0.8480 (tttt) cc_final: 0.7916 (ttpt) REVERT: B 82 GLU cc_start: 0.8067 (tt0) cc_final: 0.7587 (mm-30) REVERT: B 86 GLU cc_start: 0.8271 (tp30) cc_final: 0.7964 (tp30) REVERT: B 105 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8382 (mp) REVERT: B 115 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7976 (mtpp) REVERT: C 28 GLU cc_start: 0.8493 (mp0) cc_final: 0.8172 (mp0) REVERT: C 76 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7756 (tmtm) REVERT: C 87 LYS cc_start: 0.8555 (mttt) cc_final: 0.8303 (mtmt) REVERT: C 148 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7692 (mttt) REVERT: C 192 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8690 (mmtt) REVERT: C 220 LYS cc_start: 0.8486 (tttt) cc_final: 0.7919 (ttpt) REVERT: D 82 GLU cc_start: 0.8057 (tt0) cc_final: 0.7580 (mm-30) REVERT: D 86 GLU cc_start: 0.8268 (tp30) cc_final: 0.7962 (tp30) REVERT: D 105 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8383 (mp) REVERT: D 115 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7986 (mtpp) REVERT: F 28 GLU cc_start: 0.8487 (mp0) cc_final: 0.8166 (mp0) REVERT: F 76 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7760 (tmtm) REVERT: F 87 LYS cc_start: 0.8550 (mttt) cc_final: 0.8297 (mtmt) REVERT: F 148 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7691 (mttt) REVERT: F 192 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8691 (mmtt) REVERT: F 220 LYS cc_start: 0.8481 (tttt) cc_final: 0.7912 (ttpt) REVERT: G 82 GLU cc_start: 0.8047 (tt0) cc_final: 0.7582 (mm-30) REVERT: G 86 GLU cc_start: 0.8277 (tp30) cc_final: 0.7970 (tp30) REVERT: G 105 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8381 (mp) REVERT: G 115 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7984 (mtpp) REVERT: I 28 GLU cc_start: 0.8488 (mp0) cc_final: 0.8167 (mp0) REVERT: I 76 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7759 (tmtm) REVERT: I 87 LYS cc_start: 0.8549 (mttt) cc_final: 0.8291 (mtmt) REVERT: I 148 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7693 (mttt) REVERT: I 192 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8694 (mmtt) REVERT: I 220 LYS cc_start: 0.8484 (tttt) cc_final: 0.7914 (ttpt) REVERT: J 82 GLU cc_start: 0.8059 (tt0) cc_final: 0.7579 (mm-30) REVERT: J 86 GLU cc_start: 0.8275 (tp30) cc_final: 0.7967 (tp30) REVERT: J 105 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8380 (mp) REVERT: J 115 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7982 (mtpp) outliers start: 40 outliers final: 24 residues processed: 248 average time/residue: 0.6213 time to fit residues: 171.6457 Evaluate side-chains 248 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 296 SER Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 109 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115869 restraints weight = 85695.521| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.30 r_work: 0.3219 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17088 Z= 0.100 Angle : 0.413 4.763 22972 Z= 0.222 Chirality : 0.041 0.128 2616 Planarity : 0.003 0.036 2884 Dihedral : 10.340 87.869 2960 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.16 % Allowed : 16.30 % Favored : 81.54 % 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: 2.10 (0.19), residues: 2060 helix: 2.54 (0.17), residues: 1016 sheet: 0.99 (0.34), residues: 256 loop : 0.03 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 221 TYR 0.010 0.001 TYR A 380 PHE 0.011 0.001 PHE I 83 TRP 0.017 0.002 TRP I 315 HIS 0.003 0.001 HIS I 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (17088) covalent geometry : angle 0.41276 / 0.22 (22972) hydrogen bonds : bond 0.03852 / 2.57 ( 896) hydrogen bonds : angle 3.85533 / 2.64 ( 2520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.611 Fit side-chains REVERT: A 28 GLU cc_start: 0.8507 (mp0) cc_final: 0.8202 (mp0) REVERT: A 76 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7767 (tmtm) REVERT: A 87 LYS cc_start: 0.8519 (mttt) cc_final: 0.8264 (mtmt) REVERT: A 152 GLU cc_start: 0.7655 (tp30) cc_final: 0.6809 (mp0) REVERT: A 192 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8673 (mmtt) REVERT: A 197 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: A 220 LYS cc_start: 0.8491 (tttt) cc_final: 0.7916 (ttpt) REVERT: B 82 GLU cc_start: 0.8066 (tt0) cc_final: 0.7588 (mm-30) REVERT: B 86 GLU cc_start: 0.8237 (tp30) cc_final: 0.7946 (tp30) REVERT: B 115 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7926 (mtpp) REVERT: C 28 GLU cc_start: 0.8514 (mp0) cc_final: 0.8209 (mp0) REVERT: C 76 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7763 (tmtm) REVERT: C 87 LYS cc_start: 0.8520 (mttt) cc_final: 0.8266 (mtmt) REVERT: C 152 GLU cc_start: 0.7641 (tp30) cc_final: 0.6814 (mp0) REVERT: C 192 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8669 (mmtt) REVERT: C 197 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: C 220 LYS cc_start: 0.8486 (tttt) cc_final: 0.7915 (ttpt) REVERT: D 82 GLU cc_start: 0.8060 (tt0) cc_final: 0.7582 (mm-30) REVERT: D 86 GLU cc_start: 0.8234 (tp30) cc_final: 0.7945 (tp30) REVERT: D 115 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7937 (mtpp) REVERT: F 28 GLU cc_start: 0.8505 (mp0) cc_final: 0.8199 (mp0) REVERT: F 76 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7763 (tmtm) REVERT: F 87 LYS cc_start: 0.8517 (mttt) cc_final: 0.8262 (mtmt) REVERT: F 152 GLU cc_start: 0.7645 (tp30) cc_final: 0.6811 (mp0) REVERT: F 192 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8669 (mmtt) REVERT: F 197 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: F 220 LYS cc_start: 0.8488 (tttt) cc_final: 0.7912 (ttpt) REVERT: G 82 GLU cc_start: 0.8058 (tt0) cc_final: 0.7586 (mm-30) REVERT: G 86 GLU cc_start: 0.8246 (tp30) cc_final: 0.7957 (tp30) REVERT: G 115 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7932 (mtpp) REVERT: I 28 GLU cc_start: 0.8505 (mp0) cc_final: 0.8199 (mp0) REVERT: I 76 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7764 (tmtm) REVERT: I 87 LYS cc_start: 0.8510 (mttt) cc_final: 0.8255 (mtmt) REVERT: I 148 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7603 (mttt) REVERT: I 152 GLU cc_start: 0.7655 (tp30) cc_final: 0.6809 (mp0) REVERT: I 192 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8673 (mmtt) REVERT: I 197 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7762 (tp30) REVERT: I 220 LYS cc_start: 0.8490 (tttt) cc_final: 0.7915 (ttpt) REVERT: J 82 GLU cc_start: 0.8067 (tt0) cc_final: 0.7585 (mm-30) REVERT: J 86 GLU cc_start: 0.8240 (tp30) cc_final: 0.7950 (tp30) REVERT: J 115 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7928 (mtpp) outliers start: 37 outliers final: 16 residues processed: 253 average time/residue: 0.5901 time to fit residues: 166.5561 Evaluate side-chains 241 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain J residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 119 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114576 restraints weight = 76470.535| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.10 r_work: 0.3213 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17088 Z= 0.131 Angle : 0.448 4.775 22972 Z= 0.239 Chirality : 0.043 0.133 2616 Planarity : 0.004 0.037 2884 Dihedral : 10.314 87.191 2960 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.10 % Allowed : 16.59 % Favored : 81.31 % 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: 2.01 (0.19), residues: 2060 helix: 2.44 (0.17), residues: 1020 sheet: 0.95 (0.34), residues: 256 loop : 0.01 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 221 TYR 0.012 0.001 TYR A 380 PHE 0.012 0.001 PHE I 83 TRP 0.017 0.003 TRP A 315 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17088) covalent geometry : angle 0.44801 / 0.24 (22972) hydrogen bonds : bond 0.04495 / 3.00 ( 896) hydrogen bonds : angle 3.93627 / 2.69 ( 2520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.723 Fit side-chains REVERT: A 28 GLU cc_start: 0.8490 (mp0) cc_final: 0.8176 (mp0) REVERT: A 76 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7767 (tmtm) REVERT: A 87 LYS cc_start: 0.8544 (mttt) cc_final: 0.8288 (mtmt) REVERT: A 148 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7669 (mttt) REVERT: A 192 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8677 (mmtt) REVERT: A 197 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7768 (tp30) REVERT: A 220 LYS cc_start: 0.8465 (tttt) cc_final: 0.7916 (ttpt) REVERT: B 82 GLU cc_start: 0.8044 (tt0) cc_final: 0.7575 (mm-30) REVERT: B 86 GLU cc_start: 0.8243 (tp30) cc_final: 0.7954 (tp30) REVERT: B 105 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 115 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7957 (mtpp) REVERT: C 28 GLU cc_start: 0.8498 (mp0) cc_final: 0.8184 (mp0) REVERT: C 76 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7767 (tmtm) REVERT: C 87 LYS cc_start: 0.8541 (mttt) cc_final: 0.8287 (mtmt) REVERT: C 148 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7668 (mttt) REVERT: C 192 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8671 (mmtt) REVERT: C 197 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7772 (tp30) REVERT: C 220 LYS cc_start: 0.8478 (tttt) cc_final: 0.7922 (ttpt) REVERT: D 82 GLU cc_start: 0.8032 (tt0) cc_final: 0.7570 (mm-30) REVERT: D 86 GLU cc_start: 0.8243 (tp30) cc_final: 0.7954 (tp30) REVERT: D 105 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8390 (mp) REVERT: D 115 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7972 (mtpp) REVERT: F 28 GLU cc_start: 0.8491 (mp0) cc_final: 0.8178 (mp0) REVERT: F 76 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7771 (tmtm) REVERT: F 87 LYS cc_start: 0.8539 (mttt) cc_final: 0.8285 (mtmt) REVERT: F 148 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7663 (mttt) REVERT: F 192 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8674 (mmtt) REVERT: F 197 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: F 220 LYS cc_start: 0.8469 (tttt) cc_final: 0.7912 (ttpt) REVERT: G 82 GLU cc_start: 0.8027 (tt0) cc_final: 0.7574 (mm-30) REVERT: G 86 GLU cc_start: 0.8251 (tp30) cc_final: 0.7963 (tp30) REVERT: G 105 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8392 (mp) REVERT: G 115 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7969 (mtpp) REVERT: I 28 GLU cc_start: 0.8488 (mp0) cc_final: 0.8172 (mp0) REVERT: I 76 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7767 (tmtm) REVERT: I 87 LYS cc_start: 0.8542 (mttt) cc_final: 0.8287 (mtmt) REVERT: I 148 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7670 (mttt) REVERT: I 192 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8677 (mmtt) REVERT: I 197 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7771 (tp30) REVERT: I 220 LYS cc_start: 0.8475 (tttt) cc_final: 0.7913 (ttpt) REVERT: J 82 GLU cc_start: 0.8034 (tt0) cc_final: 0.7574 (mm-30) REVERT: J 86 GLU cc_start: 0.8249 (tp30) cc_final: 0.7961 (tp30) REVERT: J 105 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8398 (mp) REVERT: J 115 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7957 (mtpp) outliers start: 36 outliers final: 20 residues processed: 248 average time/residue: 0.6524 time to fit residues: 179.9891 Evaluate side-chains 244 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 61 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 88 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116627 restraints weight = 58705.206| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.98 r_work: 0.3238 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17088 Z= 0.099 Angle : 0.410 4.778 22972 Z= 0.220 Chirality : 0.041 0.128 2616 Planarity : 0.003 0.036 2884 Dihedral : 10.020 84.440 2960 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.75 % Allowed : 15.95 % Favored : 81.31 % 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: 2.16 (0.19), residues: 2060 helix: 2.54 (0.17), residues: 1020 sheet: 1.11 (0.35), residues: 252 loop : 0.08 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 221 TYR 0.010 0.001 TYR F 380 PHE 0.011 0.001 PHE F 83 TRP 0.017 0.002 TRP F 315 HIS 0.003 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (17088) covalent geometry : angle 0.41034 / 0.22 (22972) hydrogen bonds : bond 0.03844 / 2.56 ( 896) hydrogen bonds : angle 3.84743 / 2.63 ( 2520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.702 Fit side-chains REVERT: A 28 GLU cc_start: 0.8458 (mp0) cc_final: 0.8142 (mp0) REVERT: A 76 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7729 (tmtm) REVERT: A 87 LYS cc_start: 0.8462 (mttt) cc_final: 0.8201 (mtmt) REVERT: A 148 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7546 (mttt) REVERT: A 152 GLU cc_start: 0.7622 (tp30) cc_final: 0.6740 (mp0) REVERT: A 192 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8645 (mmtt) REVERT: A 197 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7708 (tp30) REVERT: A 220 LYS cc_start: 0.8437 (tttt) cc_final: 0.7840 (ttpt) REVERT: B 82 GLU cc_start: 0.7956 (tt0) cc_final: 0.7471 (mm-30) REVERT: B 86 GLU cc_start: 0.8164 (tp30) cc_final: 0.7854 (tp30) REVERT: B 115 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7862 (mtpp) REVERT: C 28 GLU cc_start: 0.8466 (mp0) cc_final: 0.8151 (mp0) REVERT: C 76 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7723 (tmtm) REVERT: C 87 LYS cc_start: 0.8465 (mttt) cc_final: 0.8205 (mtmt) REVERT: C 148 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7546 (mttt) REVERT: C 152 GLU cc_start: 0.7604 (tp30) cc_final: 0.6741 (mp0) REVERT: C 192 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8642 (mmtt) REVERT: C 197 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7711 (tp30) REVERT: C 220 LYS cc_start: 0.8436 (tttt) cc_final: 0.7840 (ttpt) REVERT: D 82 GLU cc_start: 0.7957 (tt0) cc_final: 0.7462 (mm-30) REVERT: D 86 GLU cc_start: 0.8161 (tp30) cc_final: 0.7852 (tp30) REVERT: D 115 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7869 (mtpp) REVERT: F 28 GLU cc_start: 0.8458 (mp0) cc_final: 0.8142 (mp0) REVERT: F 76 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7721 (tmtm) REVERT: F 87 LYS cc_start: 0.8464 (mttt) cc_final: 0.8205 (mtmt) REVERT: F 148 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7546 (mttt) REVERT: F 152 GLU cc_start: 0.7607 (tp30) cc_final: 0.6745 (mp0) REVERT: F 192 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8643 (mmtt) REVERT: F 197 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7708 (tp30) REVERT: F 220 LYS cc_start: 0.8434 (tttt) cc_final: 0.7836 (ttpt) REVERT: G 82 GLU cc_start: 0.7957 (tt0) cc_final: 0.7473 (mm-30) REVERT: G 86 GLU cc_start: 0.8170 (tp30) cc_final: 0.7861 (tp30) REVERT: G 115 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7865 (mtpp) REVERT: I 28 GLU cc_start: 0.8459 (mp0) cc_final: 0.8142 (mp0) REVERT: I 76 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7719 (tmtm) REVERT: I 87 LYS cc_start: 0.8461 (mttt) cc_final: 0.8200 (mtmt) REVERT: I 148 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7549 (mttt) REVERT: I 152 GLU cc_start: 0.7608 (tp30) cc_final: 0.6744 (mp0) REVERT: I 192 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8644 (mmtt) REVERT: I 197 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7711 (tp30) REVERT: I 220 LYS cc_start: 0.8442 (tttt) cc_final: 0.7841 (ttpt) REVERT: J 82 GLU cc_start: 0.7964 (tt0) cc_final: 0.7473 (mm-30) REVERT: J 86 GLU cc_start: 0.8161 (tp30) cc_final: 0.7852 (tp30) REVERT: J 115 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7862 (mtpp) outliers start: 47 outliers final: 27 residues processed: 259 average time/residue: 0.6704 time to fit residues: 193.5812 Evaluate side-chains 255 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112657 restraints weight = 73003.697| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.05 r_work: 0.3184 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17088 Z= 0.183 Angle : 0.513 4.785 22972 Z= 0.270 Chirality : 0.046 0.142 2616 Planarity : 0.004 0.038 2884 Dihedral : 10.622 87.648 2960 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.10 % Allowed : 16.59 % Favored : 81.31 % 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: 1.83 (0.19), residues: 2060 helix: 2.28 (0.17), residues: 1020 sheet: 0.96 (0.33), residues: 252 loop : -0.09 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 221 TYR 0.012 0.002 TYR A 380 PHE 0.014 0.002 PHE I 83 TRP 0.016 0.003 TRP A 315 HIS 0.004 0.001 HIS I 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (17088) covalent geometry : angle 0.51349 / 0.27 (22972) hydrogen bonds : bond 0.05403 / 3.60 ( 896) hydrogen bonds : angle 4.06861 / 2.79 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7184.23 seconds wall clock time: 123 minutes 15.41 seconds (7395.41 seconds total)