Starting phenix.real_space_refine on Thu May 15 16:32:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpc_47102/05_2025/9dpc_47102.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpc_47102/05_2025/9dpc_47102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dpc_47102/05_2025/9dpc_47102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpc_47102/05_2025/9dpc_47102.map" model { file = "/net/cci-nas-00/data/ceres_data/9dpc_47102/05_2025/9dpc_47102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpc_47102/05_2025/9dpc_47102.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 8459 2.51 5 N 2307 2.21 5 O 2505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13370 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2918 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 21, 'TRANS': 365} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2915 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 21, 'TRANS': 364} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2916 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 21, 'TRANS': 364} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2916 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 21, 'TRANS': 365} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 926 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 779 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 13.63, per 1000 atoms: 1.02 Number of scatterers: 13370 At special positions: 0 Unit cell: (83.053, 108.445, 139.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2505 8.00 N 2307 7.00 C 8459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.04 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.9 seconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 34 sheets defined 4.7% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.828A pdb=" N ASN A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.510A pdb=" N ASN B 146 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.859A pdb=" N ASN D 146 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.082A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.895A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 103 removed outlier: 6.444A pdb=" N SER A 444 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 125 removed outlier: 4.829A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 158 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.681A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA A 204 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR A 215 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 206 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 226 Processing sheet with id=AA5, first strand: chain 'A' and resid 225 through 226 removed outlier: 5.971A pdb=" N GLU A 259 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 284 removed outlier: 5.482A pdb=" N GLU A 278 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A 293 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 353 removed outlier: 6.708A pdb=" N LYS A 369 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLY A 395 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 389 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 103 removed outlier: 3.567A pdb=" N GLY B 96 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER B 444 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 124 removed outlier: 5.388A pdb=" N ALA B 138 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ARG B 118 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLN B 136 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 134 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE B 122 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE B 132 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS B 124 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG B 130 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 158 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 185 removed outlier: 3.776A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 204 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR B 215 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 206 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.711A pdb=" N LYS B 265 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU B 259 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 277 through 284 removed outlier: 5.523A pdb=" N GLU B 278 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG B 293 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 353 removed outlier: 6.621A pdb=" N LYS B 369 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY B 395 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 389 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 103 removed outlier: 6.398A pdb=" N SER C 444 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 117 removed outlier: 7.598A pdb=" N VAL C 116 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 117 removed outlier: 7.598A pdb=" N VAL C 116 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 158 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 180 through 185 removed outlier: 3.632A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C 204 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 215 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU C 206 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AC2, first strand: chain 'C' and resid 224 through 226 removed outlier: 3.603A pdb=" N LYS C 265 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 259 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 280 through 284 Processing sheet with id=AC4, first strand: chain 'C' and resid 350 through 353 removed outlier: 6.630A pdb=" N LYS C 369 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY C 395 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 389 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 96 through 103 removed outlier: 3.640A pdb=" N GLY D 96 " --> pdb=" O VAL D 448 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER D 444 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 115 through 117 removed outlier: 6.132A pdb=" N ALA D 138 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 115 through 117 removed outlier: 6.132A pdb=" N ALA D 138 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D 158 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.663A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR D 208 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 224 through 226 Processing sheet with id=AD1, first strand: chain 'D' and resid 224 through 226 removed outlier: 4.834A pdb=" N TYR D 253 " --> pdb=" O MET D 269 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 265 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU D 259 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 280 through 284 Processing sheet with id=AD3, first strand: chain 'D' and resid 350 through 353 removed outlier: 5.489A pdb=" N LYS D 369 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ILE D 396 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET D 373 " --> pdb=" O ASP D 392 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP D 392 " --> pdb=" O MET D 373 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TRP D 375 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS D 390 " --> pdb=" O TRP D 375 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 8.241A pdb=" N TYR H 32 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.535A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1188 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: 4.56 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4296 1.36 - 1.49: 3998 1.49 - 1.63: 5315 1.63 - 1.76: 0 1.76 - 1.90: 126 Bond restraints: 13735 Sorted by residual: bond pdb=" C LYS H 62 " pdb=" N PHE H 63 " ideal model delta sigma weight residual 1.333 1.419 -0.086 1.42e-02 4.96e+03 3.65e+01 bond pdb=" C ARG B 130 " pdb=" N THR B 131 " ideal model delta sigma weight residual 1.330 1.399 -0.069 1.40e-02 5.10e+03 2.42e+01 bond pdb=" C TRP D 296 " pdb=" N HIS D 297 " ideal model delta sigma weight residual 1.332 1.268 0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" CA PHE L 98 " pdb=" C PHE L 98 " ideal model delta sigma weight residual 1.524 1.469 0.056 1.29e-02 6.01e+03 1.87e+01 bond pdb=" C ASP B 142 " pdb=" N LYS B 143 " ideal model delta sigma weight residual 1.333 1.272 0.061 1.49e-02 4.50e+03 1.67e+01 ... (remaining 13730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 18322 2.06 - 4.12: 302 4.12 - 6.17: 44 6.17 - 8.23: 10 8.23 - 10.29: 4 Bond angle restraints: 18682 Sorted by residual: angle pdb=" O LYS H 62 " pdb=" C LYS H 62 " pdb=" N PHE H 63 " ideal model delta sigma weight residual 122.12 128.43 -6.31 1.06e+00 8.90e-01 3.54e+01 angle pdb=" N GLY C 429 " pdb=" CA GLY C 429 " pdb=" C GLY C 429 " ideal model delta sigma weight residual 110.20 118.00 -7.80 1.32e+00 5.74e-01 3.49e+01 angle pdb=" C LYS H 62 " pdb=" N PHE H 63 " pdb=" CA PHE H 63 " ideal model delta sigma weight residual 122.86 114.95 7.91 1.53e+00 4.27e-01 2.67e+01 angle pdb=" CA PHE L 98 " pdb=" CB PHE L 98 " pdb=" CG PHE L 98 " ideal model delta sigma weight residual 113.80 118.96 -5.16 1.00e+00 1.00e+00 2.66e+01 angle pdb=" N PHE L 98 " pdb=" CA PHE L 98 " pdb=" CB PHE L 98 " ideal model delta sigma weight residual 111.20 103.28 7.92 1.65e+00 3.67e-01 2.31e+01 ... (remaining 18677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 6901 17.63 - 35.27: 874 35.27 - 52.90: 246 52.90 - 70.53: 40 70.53 - 88.17: 7 Dihedral angle restraints: 8068 sinusoidal: 3036 harmonic: 5032 Sorted by residual: dihedral pdb=" CB CYS C 92 " pdb=" SG CYS C 92 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual 93.00 12.22 80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 184 " pdb=" SG CYS B 184 " pdb=" SG CYS B 231 " pdb=" CB CYS B 231 " ideal model delta sinusoidal sigma weight residual 93.00 139.65 -46.65 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CA ASN B 309 " pdb=" C ASN B 309 " pdb=" N LEU B 310 " pdb=" CA LEU B 310 " ideal model delta harmonic sigma weight residual 180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 8065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1573 0.053 - 0.106: 330 0.106 - 0.158: 97 0.158 - 0.211: 6 0.211 - 0.264: 2 Chirality restraints: 2008 Sorted by residual: chirality pdb=" CA LYS C 331 " pdb=" N LYS C 331 " pdb=" C LYS C 331 " pdb=" CB LYS C 331 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA HIS D 297 " pdb=" N HIS D 297 " pdb=" C HIS D 297 " pdb=" CB HIS D 297 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL C 234 " pdb=" N VAL C 234 " pdb=" C VAL C 234 " pdb=" CB VAL C 234 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2005 not shown) Planarity restraints: 2393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN H 61 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C GLN H 61 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN H 61 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS H 62 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 63 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C PHE H 63 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE H 63 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN H 64 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 368 " -0.207 9.50e-02 1.11e+02 9.26e-02 5.27e+00 pdb=" NE ARG C 368 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 368 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 368 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 368 " -0.007 2.00e-02 2.50e+03 ... (remaining 2390 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1125 2.74 - 3.28: 12226 3.28 - 3.82: 22813 3.82 - 4.36: 28922 4.36 - 4.90: 50607 Nonbonded interactions: 115693 Sorted by model distance: nonbonded pdb=" OD1 ASN D 355 " pdb=" OG1 THR D 381 " model vdw 2.198 3.040 nonbonded pdb=" OE1 GLU A 372 " pdb=" NZ LYS A 390 " model vdw 2.203 3.120 nonbonded pdb=" OG SER L 77 " pdb=" OE1 GLN L 79 " model vdw 2.206 3.040 nonbonded pdb=" NH2 ARG D 152 " pdb=" O ILE H 100B" model vdw 2.245 3.120 nonbonded pdb=" OG SER D 364 " pdb=" O SER D 367 " model vdw 2.249 3.040 ... (remaining 115688 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 83 through 149 or (resid 150 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 151 through 261 or (resid 262 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD )) or \ resid 263 through 452 or (resid 453 and (name N or name CA or name C or name O o \ r name CB )) or resid 454 through 461 or (resid 462 and (name N or name CA or na \ me C or name O or name CB )) or resid 463 through 468)) selection = (chain 'B' and (resid 83 through 149 or (resid 150 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 151 through 259 or (resid 260 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 261 o \ r (resid 262 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or resid 263 through 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 387 through 461 or (r \ esid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 t \ hrough 468)) selection = (chain 'C' and (resid 83 through 149 or (resid 150 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 151 through 259 or (resid 260 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 261 o \ r (resid 262 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or resid 263 through 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 387 through 452 or (r \ esid 453 and (name N or name CA or name C or name O or name CB )) or resid 454 t \ hrough 461 or (resid 462 and (name N or name CA or name C or name O or name CB ) \ ) or resid 463 through 468)) selection = (chain 'D' and (resid 83 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 259 or (resid 260 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 261 through 385 \ or (resid 386 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD )) or resid 387 through 452 or (resid 453 and (name N or name CA or na \ me C or name O or name CB )) or resid 454 through 468)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 37.470 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: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 38.000 Find NCS groups from input model: 0.810 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:14.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.004 0.087 13766 Z= 0.218 Angle : 0.649 10.290 18744 Z= 0.368 Chirality : 0.048 0.264 2008 Planarity : 0.005 0.093 2393 Dihedral : 16.565 88.169 4775 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.95 % Allowed : 27.21 % Favored : 69.85 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 1765 helix: -2.71 (0.56), residues: 52 sheet: 0.40 (0.20), residues: 672 loop : -1.53 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 219 HIS 0.004 0.001 HIS D 297 PHE 0.014 0.001 PHE B 406 TYR 0.018 0.001 TYR A 274 ARG 0.005 0.000 ARG C 130 Details of bonding type rmsd hydrogen bonds : bond 0.09197 ( 453) hydrogen bonds : angle 7.48513 ( 1188) SS BOND : bond 0.00275 ( 31) SS BOND : angle 1.36499 ( 62) covalent geometry : bond 0.00386 (13735) covalent geometry : angle 0.64531 (18682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 445 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 SER cc_start: 0.8374 (t) cc_final: 0.8014 (p) REVERT: A 173 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: A 277 GLU cc_start: 0.7789 (tt0) cc_final: 0.7360 (tt0) REVERT: A 453 MET cc_start: 0.8328 (tpp) cc_final: 0.7904 (tpp) REVERT: B 148 THR cc_start: 0.7067 (m) cc_final: 0.6855 (p) REVERT: B 176 SER cc_start: 0.8312 (p) cc_final: 0.8101 (m) REVERT: B 378 ASN cc_start: 0.7480 (p0) cc_final: 0.7233 (p0) REVERT: B 411 GLU cc_start: 0.7310 (mp0) cc_final: 0.6874 (mp0) REVERT: C 268 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7241 (tm-30) REVERT: C 273 ASN cc_start: 0.8035 (t0) cc_final: 0.7633 (t0) REVERT: C 357 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8186 (p) REVERT: C 411 GLU cc_start: 0.7673 (mp0) cc_final: 0.7348 (mp0) REVERT: D 173 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7349 (ttp80) REVERT: D 175 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: D 189 ASN cc_start: 0.7637 (m-40) cc_final: 0.7228 (m-40) REVERT: D 213 THR cc_start: 0.8417 (m) cc_final: 0.8086 (p) REVERT: D 233 CYS cc_start: 0.6739 (m) cc_final: 0.6456 (m) REVERT: D 330 ASP cc_start: 0.7450 (m-30) cc_final: 0.7155 (m-30) REVERT: D 361 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7902 (ptm160) REVERT: H 79 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6789 (p0) outliers start: 42 outliers final: 29 residues processed: 465 average time/residue: 1.0923 time to fit residues: 558.5759 Evaluate side-chains 468 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 435 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 91 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 0.0470 chunk 82 optimal weight: 0.0070 chunk 101 optimal weight: 0.1980 chunk 158 optimal weight: 2.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN C 295 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109396 restraints weight = 18251.880| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.56 r_work: 0.3411 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13766 Z= 0.140 Angle : 0.568 11.166 18744 Z= 0.292 Chirality : 0.046 0.157 2008 Planarity : 0.004 0.041 2393 Dihedral : 6.266 59.101 1953 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.93 % Allowed : 24.54 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1765 helix: -2.66 (0.53), residues: 52 sheet: 0.58 (0.20), residues: 658 loop : -1.53 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 358 HIS 0.004 0.001 HIS B 297 PHE 0.016 0.001 PHE B 406 TYR 0.012 0.001 TYR C 253 ARG 0.005 0.000 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 453) hydrogen bonds : angle 6.20669 ( 1188) SS BOND : bond 0.00395 ( 31) SS BOND : angle 1.17688 ( 62) covalent geometry : bond 0.00327 (13735) covalent geometry : angle 0.56488 (18682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 448 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7575 (ttm-80) REVERT: A 189 ASN cc_start: 0.8208 (m-40) cc_final: 0.7790 (m-40) REVERT: A 277 GLU cc_start: 0.7843 (tt0) cc_final: 0.7513 (tt0) REVERT: A 411 GLU cc_start: 0.7801 (mp0) cc_final: 0.7389 (mp0) REVERT: A 453 MET cc_start: 0.8342 (tpp) cc_final: 0.7924 (tpp) REVERT: B 148 THR cc_start: 0.7117 (m) cc_final: 0.6908 (p) REVERT: B 411 GLU cc_start: 0.7337 (mp0) cc_final: 0.6888 (mp0) REVERT: C 175 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7218 (mm-30) REVERT: C 268 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7221 (tm-30) REVERT: C 273 ASN cc_start: 0.8102 (t0) cc_final: 0.7748 (t0) REVERT: C 357 VAL cc_start: 0.8378 (t) cc_final: 0.8139 (p) REVERT: C 411 GLU cc_start: 0.7639 (mp0) cc_final: 0.7349 (mp0) REVERT: C 428 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8197 (mtp180) REVERT: D 108 ILE cc_start: 0.8357 (mt) cc_final: 0.8157 (mm) REVERT: D 173 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7155 (ttp80) REVERT: D 175 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: D 189 ASN cc_start: 0.7659 (m-40) cc_final: 0.7327 (m-40) REVERT: D 233 CYS cc_start: 0.6703 (m) cc_final: 0.6437 (m) REVERT: D 330 ASP cc_start: 0.7460 (m-30) cc_final: 0.7126 (m-30) outliers start: 56 outliers final: 24 residues processed: 478 average time/residue: 1.0383 time to fit residues: 549.0187 Evaluate side-chains 460 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 435 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 28 optimal weight: 0.0670 chunk 129 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN A 295 ASN B 273 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 297 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109572 restraints weight = 18364.681| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.56 r_work: 0.3418 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13766 Z= 0.142 Angle : 0.571 10.851 18744 Z= 0.292 Chirality : 0.046 0.160 2008 Planarity : 0.004 0.041 2393 Dihedral : 5.707 59.150 1918 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.30 % Allowed : 25.39 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1765 helix: -2.57 (0.54), residues: 52 sheet: 0.65 (0.20), residues: 658 loop : -1.52 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 358 HIS 0.004 0.001 HIS B 297 PHE 0.015 0.001 PHE B 406 TYR 0.012 0.001 TYR C 253 ARG 0.009 0.000 ARG B 220 Details of bonding type rmsd hydrogen bonds : bond 0.02973 ( 453) hydrogen bonds : angle 6.01706 ( 1188) SS BOND : bond 0.00533 ( 31) SS BOND : angle 1.24631 ( 62) covalent geometry : bond 0.00331 (13735) covalent geometry : angle 0.56785 (18682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 447 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 CYS cc_start: 0.5649 (OUTLIER) cc_final: 0.5348 (p) REVERT: A 277 GLU cc_start: 0.7816 (tt0) cc_final: 0.7514 (tt0) REVERT: A 411 GLU cc_start: 0.7814 (mp0) cc_final: 0.7398 (mp0) REVERT: A 453 MET cc_start: 0.8364 (tpp) cc_final: 0.7961 (tpp) REVERT: B 148 THR cc_start: 0.7095 (m) cc_final: 0.6889 (p) REVERT: B 411 GLU cc_start: 0.7333 (mp0) cc_final: 0.6891 (mp0) REVERT: C 175 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7208 (mm-30) REVERT: C 176 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8486 (p) REVERT: C 268 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7182 (tm-30) REVERT: C 273 ASN cc_start: 0.8136 (t0) cc_final: 0.7776 (t0) REVERT: C 357 VAL cc_start: 0.8365 (t) cc_final: 0.8127 (p) REVERT: C 411 GLU cc_start: 0.7633 (mp0) cc_final: 0.7339 (mp0) REVERT: C 428 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8229 (mtp180) REVERT: D 108 ILE cc_start: 0.8372 (mt) cc_final: 0.8161 (mm) REVERT: D 173 ARG cc_start: 0.7826 (ttp80) cc_final: 0.7116 (ttp80) REVERT: D 175 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: D 189 ASN cc_start: 0.7655 (m-40) cc_final: 0.7277 (m-40) REVERT: D 213 THR cc_start: 0.8376 (m) cc_final: 0.8062 (p) REVERT: D 233 CYS cc_start: 0.6690 (m) cc_final: 0.6417 (m) REVERT: D 330 ASP cc_start: 0.7446 (m-30) cc_final: 0.7111 (m-30) outliers start: 47 outliers final: 29 residues processed: 468 average time/residue: 1.0424 time to fit residues: 538.8151 Evaluate side-chains 473 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 441 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 39 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 133 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B 341 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 297 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.116690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.108591 restraints weight = 18128.452| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.53 r_work: 0.3403 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.005 0.089 13766 Z= 0.200 Angle : 0.606 11.150 18744 Z= 0.310 Chirality : 0.048 0.164 2008 Planarity : 0.004 0.042 2393 Dihedral : 5.871 59.890 1917 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.28 % Allowed : 24.82 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1765 helix: -2.63 (0.51), residues: 52 sheet: 0.61 (0.20), residues: 640 loop : -1.49 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 358 HIS 0.006 0.001 HIS B 297 PHE 0.018 0.002 PHE B 406 TYR 0.013 0.001 TYR C 253 ARG 0.006 0.000 ARG B 220 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 453) hydrogen bonds : angle 6.14008 ( 1188) SS BOND : bond 0.00568 ( 31) SS BOND : angle 1.38412 ( 62) covalent geometry : bond 0.00464 (13735) covalent geometry : angle 0.60160 (18682) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 435 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.7834 (tt0) cc_final: 0.7536 (tt0) REVERT: A 369 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8223 (mtpp) REVERT: A 411 GLU cc_start: 0.7811 (mp0) cc_final: 0.7393 (mp0) REVERT: A 453 MET cc_start: 0.8347 (tpp) cc_final: 0.7941 (tpp) REVERT: B 148 THR cc_start: 0.7237 (m) cc_final: 0.6992 (p) REVERT: B 378 ASN cc_start: 0.7506 (p0) cc_final: 0.7256 (p0) REVERT: B 411 GLU cc_start: 0.7306 (mp0) cc_final: 0.6867 (mp0) REVERT: C 175 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7275 (mm-30) REVERT: C 176 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8504 (p) REVERT: C 268 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7232 (tm-30) REVERT: C 273 ASN cc_start: 0.8060 (t0) cc_final: 0.7703 (t0) REVERT: C 294 ASP cc_start: 0.7077 (t0) cc_final: 0.6693 (t0) REVERT: C 316 TYR cc_start: 0.8526 (m-80) cc_final: 0.8309 (m-80) REVERT: C 357 VAL cc_start: 0.8407 (t) cc_final: 0.8146 (p) REVERT: C 411 GLU cc_start: 0.7633 (mp0) cc_final: 0.7319 (mp0) REVERT: C 428 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8187 (mtp180) REVERT: D 108 ILE cc_start: 0.8378 (mt) cc_final: 0.8170 (mm) REVERT: D 173 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7138 (ttp80) REVERT: D 175 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: D 189 ASN cc_start: 0.7662 (m-40) cc_final: 0.7262 (m-40) REVERT: D 330 ASP cc_start: 0.7456 (m-30) cc_final: 0.7119 (m-30) outliers start: 61 outliers final: 45 residues processed: 468 average time/residue: 1.0493 time to fit residues: 543.8619 Evaluate side-chains 477 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 430 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 162 optimal weight: 0.0470 chunk 138 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 120 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.109790 restraints weight = 18174.420| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.54 r_work: 0.3421 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13766 Z= 0.132 Angle : 0.572 11.473 18744 Z= 0.292 Chirality : 0.046 0.155 2008 Planarity : 0.004 0.040 2393 Dihedral : 5.679 59.706 1917 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.51 % Allowed : 26.09 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1765 helix: -2.46 (0.56), residues: 52 sheet: 0.71 (0.20), residues: 634 loop : -1.50 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 358 HIS 0.003 0.001 HIS B 297 PHE 0.014 0.001 PHE B 406 TYR 0.012 0.001 TYR C 253 ARG 0.007 0.000 ARG B 220 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 453) hydrogen bonds : angle 5.96565 ( 1188) SS BOND : bond 0.00495 ( 31) SS BOND : angle 1.35294 ( 62) covalent geometry : bond 0.00312 (13735) covalent geometry : angle 0.56810 (18682) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 442 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.7839 (tt0) cc_final: 0.7551 (tt0) REVERT: A 411 GLU cc_start: 0.7794 (mp0) cc_final: 0.7387 (mp0) REVERT: A 453 MET cc_start: 0.8339 (tpp) cc_final: 0.7953 (tpp) REVERT: B 107 ARG cc_start: 0.8776 (mtp85) cc_final: 0.8567 (mtp85) REVERT: B 148 THR cc_start: 0.7076 (m) cc_final: 0.6870 (p) REVERT: B 378 ASN cc_start: 0.7285 (p0) cc_final: 0.7055 (p0) REVERT: B 411 GLU cc_start: 0.7298 (mp0) cc_final: 0.6852 (mp0) REVERT: C 175 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7264 (mm-30) REVERT: C 268 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7206 (tm-30) REVERT: C 273 ASN cc_start: 0.8050 (t0) cc_final: 0.7689 (t0) REVERT: C 294 ASP cc_start: 0.7046 (t0) cc_final: 0.6652 (t0) REVERT: C 357 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8152 (p) REVERT: C 411 GLU cc_start: 0.7639 (mp0) cc_final: 0.7339 (mp0) REVERT: C 433 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7346 (mt-10) REVERT: D 108 ILE cc_start: 0.8356 (mt) cc_final: 0.8141 (mm) REVERT: D 173 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7138 (ttp80) REVERT: D 175 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: D 189 ASN cc_start: 0.7643 (m-40) cc_final: 0.7308 (m-40) REVERT: D 213 THR cc_start: 0.8370 (m) cc_final: 0.8090 (p) REVERT: D 330 ASP cc_start: 0.7452 (m-30) cc_final: 0.7123 (m-30) REVERT: D 453 MET cc_start: 0.8260 (tpp) cc_final: 0.7951 (tpp) outliers start: 50 outliers final: 37 residues processed: 469 average time/residue: 1.0552 time to fit residues: 546.3968 Evaluate side-chains 463 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 424 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 27 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B 341 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS D 409 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.107668 restraints weight = 18319.822| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.53 r_work: 0.3382 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 13766 Z= 0.260 Angle : 0.649 13.283 18744 Z= 0.331 Chirality : 0.049 0.190 2008 Planarity : 0.005 0.042 2393 Dihedral : 6.062 59.678 1917 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.28 % Allowed : 25.53 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1765 helix: -2.78 (0.48), residues: 52 sheet: 0.52 (0.20), residues: 658 loop : -1.57 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 358 HIS 0.006 0.001 HIS B 297 PHE 0.021 0.002 PHE B 406 TYR 0.014 0.002 TYR C 253 ARG 0.007 0.001 ARG B 220 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 453) hydrogen bonds : angle 6.21495 ( 1188) SS BOND : bond 0.00736 ( 31) SS BOND : angle 1.67463 ( 62) covalent geometry : bond 0.00602 (13735) covalent geometry : angle 0.64299 (18682) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 431 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.7863 (tt0) cc_final: 0.7568 (tt0) REVERT: A 453 MET cc_start: 0.8363 (tpp) cc_final: 0.7977 (tpp) REVERT: B 148 THR cc_start: 0.7350 (m) cc_final: 0.7093 (p) REVERT: B 407 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8513 (m) REVERT: B 411 GLU cc_start: 0.7311 (mp0) cc_final: 0.6858 (mp0) REVERT: C 156 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7382 (mtt180) REVERT: C 175 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 268 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7219 (tm-30) REVERT: C 273 ASN cc_start: 0.8061 (t0) cc_final: 0.7712 (t0) REVERT: C 357 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8151 (p) REVERT: C 411 GLU cc_start: 0.7651 (mp0) cc_final: 0.7336 (mp0) REVERT: D 108 ILE cc_start: 0.8375 (mt) cc_final: 0.8171 (mm) REVERT: D 175 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: D 189 ASN cc_start: 0.7690 (m-40) cc_final: 0.7356 (m-40) REVERT: D 213 THR cc_start: 0.8383 (m) cc_final: 0.8083 (p) REVERT: D 330 ASP cc_start: 0.7444 (m-30) cc_final: 0.7111 (m-30) outliers start: 61 outliers final: 44 residues processed: 469 average time/residue: 1.0717 time to fit residues: 554.3538 Evaluate side-chains 463 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 415 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 141 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 169 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 150 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.117017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108939 restraints weight = 18210.728| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.54 r_work: 0.3408 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 13766 Z= 0.176 Angle : 0.612 13.187 18744 Z= 0.311 Chirality : 0.047 0.187 2008 Planarity : 0.004 0.042 2393 Dihedral : 5.884 59.568 1917 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.37 % Allowed : 26.51 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.19), residues: 1765 helix: -2.77 (0.48), residues: 52 sheet: 0.49 (0.20), residues: 664 loop : -1.56 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 358 HIS 0.004 0.001 HIS B 297 PHE 0.017 0.002 PHE B 406 TYR 0.015 0.001 TYR A 274 ARG 0.007 0.001 ARG C 428 Details of bonding type rmsd hydrogen bonds : bond 0.03079 ( 453) hydrogen bonds : angle 6.06999 ( 1188) SS BOND : bond 0.00602 ( 31) SS BOND : angle 1.60584 ( 62) covalent geometry : bond 0.00410 (13735) covalent geometry : angle 0.60624 (18682) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 431 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.7853 (tt0) cc_final: 0.7556 (tt0) REVERT: A 411 GLU cc_start: 0.7814 (mp0) cc_final: 0.7392 (mp0) REVERT: A 453 MET cc_start: 0.8321 (tpp) cc_final: 0.7934 (tpp) REVERT: B 148 THR cc_start: 0.7256 (m) cc_final: 0.7028 (p) REVERT: B 411 GLU cc_start: 0.7314 (mp0) cc_final: 0.6868 (mp0) REVERT: C 156 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7369 (mtt180) REVERT: C 175 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 268 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7207 (tm-30) REVERT: C 273 ASN cc_start: 0.8051 (t0) cc_final: 0.7694 (t0) REVERT: C 294 ASP cc_start: 0.7017 (t0) cc_final: 0.6671 (t0) REVERT: C 357 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8150 (p) REVERT: C 411 GLU cc_start: 0.7638 (mp0) cc_final: 0.7332 (mp0) REVERT: D 108 ILE cc_start: 0.8366 (mt) cc_final: 0.8154 (mm) REVERT: D 173 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7140 (ttp80) REVERT: D 175 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: D 189 ASN cc_start: 0.7644 (m-40) cc_final: 0.7290 (m-40) REVERT: D 330 ASP cc_start: 0.7449 (m-30) cc_final: 0.7131 (m-30) outliers start: 48 outliers final: 40 residues processed: 459 average time/residue: 1.0648 time to fit residues: 539.6421 Evaluate side-chains 469 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 426 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 22 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 341 ASN B 295 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.115524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107396 restraints weight = 18340.354| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.54 r_work: 0.3383 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 13766 Z= 0.272 Angle : 0.664 13.808 18744 Z= 0.339 Chirality : 0.050 0.209 2008 Planarity : 0.005 0.046 2393 Dihedral : 6.138 59.157 1917 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.07 % Allowed : 25.95 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 1765 helix: -3.08 (0.42), residues: 52 sheet: 0.49 (0.20), residues: 654 loop : -1.60 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 358 HIS 0.007 0.001 HIS B 297 PHE 0.022 0.002 PHE B 406 TYR 0.017 0.002 TYR C 253 ARG 0.006 0.001 ARG B 220 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 453) hydrogen bonds : angle 6.22772 ( 1188) SS BOND : bond 0.00700 ( 31) SS BOND : angle 1.70620 ( 62) covalent geometry : bond 0.00629 (13735) covalent geometry : angle 0.65759 (18682) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 430 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.7915 (t0) cc_final: 0.7697 (t0) REVERT: A 277 GLU cc_start: 0.7886 (tt0) cc_final: 0.7565 (tt0) REVERT: A 453 MET cc_start: 0.8343 (tpp) cc_final: 0.7974 (tpp) REVERT: B 148 THR cc_start: 0.7458 (m) cc_final: 0.7218 (p) REVERT: B 407 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8522 (m) REVERT: B 411 GLU cc_start: 0.7327 (mp0) cc_final: 0.6885 (mp0) REVERT: C 156 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7394 (mtt180) REVERT: C 175 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7285 (mm-30) REVERT: C 268 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7219 (tm-30) REVERT: C 273 ASN cc_start: 0.8056 (t0) cc_final: 0.7714 (t0) REVERT: C 316 TYR cc_start: 0.8607 (m-80) cc_final: 0.8351 (m-80) REVERT: C 357 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8146 (p) REVERT: C 411 GLU cc_start: 0.7652 (mp0) cc_final: 0.7337 (mp0) REVERT: D 108 ILE cc_start: 0.8374 (mt) cc_final: 0.8163 (mm) REVERT: D 175 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: D 189 ASN cc_start: 0.7688 (m-40) cc_final: 0.7320 (m-40) REVERT: D 213 THR cc_start: 0.8407 (m) cc_final: 0.8120 (p) REVERT: D 330 ASP cc_start: 0.7442 (m-30) cc_final: 0.7107 (m-30) outliers start: 58 outliers final: 42 residues processed: 463 average time/residue: 1.0262 time to fit residues: 530.1170 Evaluate side-chains 473 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 427 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 91 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 173 optimal weight: 0.0980 chunk 111 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 295 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108889 restraints weight = 18073.143| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.53 r_work: 0.3404 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13766 Z= 0.187 Angle : 0.622 13.949 18744 Z= 0.318 Chirality : 0.048 0.207 2008 Planarity : 0.004 0.050 2393 Dihedral : 5.932 59.056 1917 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.37 % Allowed : 26.72 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 1765 helix: -2.95 (0.44), residues: 52 sheet: 0.51 (0.20), residues: 654 loop : -1.58 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 358 HIS 0.004 0.001 HIS B 297 PHE 0.017 0.002 PHE B 406 TYR 0.016 0.001 TYR A 274 ARG 0.009 0.001 ARG C 428 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 453) hydrogen bonds : angle 6.09629 ( 1188) SS BOND : bond 0.00605 ( 31) SS BOND : angle 1.48526 ( 62) covalent geometry : bond 0.00435 (13735) covalent geometry : angle 0.61749 (18682) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 430 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.7854 (tt0) cc_final: 0.7560 (tt0) REVERT: A 411 GLU cc_start: 0.7818 (mp0) cc_final: 0.7395 (mp0) REVERT: A 438 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 453 MET cc_start: 0.8343 (tpp) cc_final: 0.7977 (tpp) REVERT: B 148 THR cc_start: 0.7349 (m) cc_final: 0.7098 (p) REVERT: B 411 GLU cc_start: 0.7316 (mp0) cc_final: 0.6859 (mp0) REVERT: C 156 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7337 (mtt180) REVERT: C 175 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7283 (mm-30) REVERT: C 268 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7205 (tm-30) REVERT: C 273 ASN cc_start: 0.8032 (t0) cc_final: 0.7684 (t0) REVERT: C 294 ASP cc_start: 0.6962 (t0) cc_final: 0.6646 (t0) REVERT: C 357 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8148 (p) REVERT: C 411 GLU cc_start: 0.7640 (mp0) cc_final: 0.7340 (mp0) REVERT: D 108 ILE cc_start: 0.8372 (mt) cc_final: 0.8155 (mm) REVERT: D 175 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: D 189 ASN cc_start: 0.7647 (m-40) cc_final: 0.7274 (m-40) REVERT: D 213 THR cc_start: 0.8410 (m) cc_final: 0.8109 (p) REVERT: D 330 ASP cc_start: 0.7442 (m-30) cc_final: 0.7127 (m-30) outliers start: 48 outliers final: 37 residues processed: 457 average time/residue: 1.0827 time to fit residues: 545.3745 Evaluate side-chains 464 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 423 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 107 optimal weight: 0.9980 chunk 80 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 8 optimal weight: 0.0270 chunk 20 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN B 295 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109817 restraints weight = 18129.820| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.54 r_work: 0.3422 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 13766 Z= 0.145 Angle : 0.603 12.833 18744 Z= 0.308 Chirality : 0.047 0.180 2008 Planarity : 0.004 0.053 2393 Dihedral : 5.771 58.962 1917 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.88 % Allowed : 27.35 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1765 helix: -2.78 (0.48), residues: 52 sheet: 0.63 (0.20), residues: 642 loop : -1.53 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 358 HIS 0.004 0.001 HIS B 297 PHE 0.015 0.001 PHE B 406 TYR 0.014 0.001 TYR C 253 ARG 0.005 0.000 ARG C 428 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 453) hydrogen bonds : angle 6.01042 ( 1188) SS BOND : bond 0.00572 ( 31) SS BOND : angle 1.50372 ( 62) covalent geometry : bond 0.00342 (13735) covalent geometry : angle 0.59771 (18682) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 438 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.7851 (tt0) cc_final: 0.7583 (tt0) REVERT: A 411 GLU cc_start: 0.7794 (mp0) cc_final: 0.7378 (mp0) REVERT: A 438 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 453 MET cc_start: 0.8342 (tpp) cc_final: 0.7978 (tpp) REVERT: B 148 THR cc_start: 0.7233 (m) cc_final: 0.7002 (p) REVERT: B 411 GLU cc_start: 0.7293 (mp0) cc_final: 0.6834 (mp0) REVERT: C 156 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7330 (mtt180) REVERT: C 175 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7307 (mm-30) REVERT: C 268 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7193 (tm-30) REVERT: C 273 ASN cc_start: 0.8049 (t0) cc_final: 0.7709 (t0) REVERT: C 316 TYR cc_start: 0.8467 (m-80) cc_final: 0.8259 (m-80) REVERT: C 357 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8157 (p) REVERT: C 411 GLU cc_start: 0.7638 (mp0) cc_final: 0.7356 (mp0) REVERT: C 428 ARG cc_start: 0.8251 (mtp180) cc_final: 0.8047 (mmm160) REVERT: D 108 ILE cc_start: 0.8359 (mt) cc_final: 0.8135 (mm) REVERT: D 175 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: D 189 ASN cc_start: 0.7627 (m-40) cc_final: 0.7249 (m-40) REVERT: D 213 THR cc_start: 0.8375 (m) cc_final: 0.8118 (p) REVERT: D 330 ASP cc_start: 0.7431 (m-30) cc_final: 0.7116 (m-30) REVERT: D 453 MET cc_start: 0.8253 (tpp) cc_final: 0.7945 (tpp) outliers start: 41 outliers final: 33 residues processed: 460 average time/residue: 1.1284 time to fit residues: 571.2404 Evaluate side-chains 472 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 435 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 11 optimal weight: 0.0370 chunk 150 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.108932 restraints weight = 18235.304| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.54 r_work: 0.3405 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 13766 Z= 0.197 Angle : 0.640 13.171 18744 Z= 0.325 Chirality : 0.048 0.200 2008 Planarity : 0.004 0.055 2393 Dihedral : 5.915 58.501 1917 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.95 % Allowed : 27.91 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1765 helix: -2.84 (0.47), residues: 52 sheet: 0.56 (0.21), residues: 630 loop : -1.55 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 219 HIS 0.005 0.001 HIS B 297 PHE 0.018 0.002 PHE B 465 TYR 0.015 0.001 TYR C 253 ARG 0.005 0.001 ARG B 220 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 453) hydrogen bonds : angle 6.09044 ( 1188) SS BOND : bond 0.00669 ( 31) SS BOND : angle 1.60042 ( 62) covalent geometry : bond 0.00461 (13735) covalent geometry : angle 0.63475 (18682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13541.78 seconds wall clock time: 234 minutes 22.96 seconds (14062.96 seconds total)