Starting phenix.real_space_refine on Thu Sep 18 02:39:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpc_47102/09_2025/9dpc_47102.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpc_47102/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dpc_47102/09_2025/9dpc_47102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpc_47102/09_2025/9dpc_47102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dpc_47102/09_2025/9dpc_47102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpc_47102/09_2025/9dpc_47102.map" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 10, 'GLU:plan': 8, 'ASN:plan1': 2} 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: {'ASP:plan': 10, 'GLU:plan': 8, 'ASN:plan1': 1} 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: {'ASP:plan': 10, 'GLU:plan': 8, 'ASN:plan1': 1} 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: {'ASP:plan': 10, 'GLU:plan': 8, 'ASN:plan1': 2} 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, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG: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: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 3.41, per 1000 atoms: 0.26 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: 1.02 Conformation dependent library (CDL) restraints added in 630.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.58 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: 2.60 Time building geometry restraints manager: 1.37 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: 35.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.930 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.390 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG C 130 TYR 0.018 0.001 TYR A 274 PHE 0.014 0.001 PHE B 406 TRP 0.016 0.001 TRP D 219 HIS 0.004 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00386 (13735) covalent geometry : angle 0.64531 (18682) SS BOND : bond 0.00275 ( 31) SS BOND : angle 1.36499 ( 62) hydrogen bonds : bond 0.09197 ( 453) hydrogen bonds : angle 7.48513 ( 1188) *********************** 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 : 0.578 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: 0.5764 time to fit residues: 294.5927 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 : 0.572 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.0060 overall best weight: 0.3172 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.117888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109742 restraints weight = 18268.223| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.55 r_work: 0.3414 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13766 Z= 0.133 Angle : 0.563 11.162 18744 Z= 0.290 Chirality : 0.046 0.157 2008 Planarity : 0.004 0.041 2393 Dihedral : 6.229 59.212 1953 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.93 % Allowed : 24.40 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.19), residues: 1765 helix: -2.64 (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 ARG 0.004 0.000 ARG B 419 TYR 0.012 0.001 TYR C 253 PHE 0.016 0.001 PHE B 406 TRP 0.013 0.001 TRP D 358 HIS 0.004 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00309 (13735) covalent geometry : angle 0.56044 (18682) SS BOND : bond 0.00401 ( 31) SS BOND : angle 1.08116 ( 62) hydrogen bonds : bond 0.03058 ( 453) hydrogen bonds : angle 6.17528 ( 1188) *********************** 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 507 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 451 time to evaluate : 0.512 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: 0.7886 (ttm-80) cc_final: 0.7569 (ttm-80) REVERT: A 189 ASN cc_start: 0.8191 (m-40) cc_final: 0.7771 (m-40) REVERT: A 277 GLU cc_start: 0.7835 (tt0) cc_final: 0.7507 (tt0) REVERT: A 411 GLU cc_start: 0.7803 (mp0) cc_final: 0.7395 (mp0) REVERT: A 453 MET cc_start: 0.8326 (tpp) cc_final: 0.7904 (tpp) REVERT: B 148 THR cc_start: 0.7110 (m) cc_final: 0.6902 (p) REVERT: B 411 GLU cc_start: 0.7337 (mp0) cc_final: 0.6890 (mp0) REVERT: C 175 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7219 (mm-30) REVERT: C 268 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7214 (tm-30) REVERT: C 273 ASN cc_start: 0.8097 (t0) cc_final: 0.7746 (t0) REVERT: C 357 VAL cc_start: 0.8375 (t) cc_final: 0.8139 (p) REVERT: C 411 GLU cc_start: 0.7629 (mp0) cc_final: 0.7341 (mp0) REVERT: C 428 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8200 (mtp180) REVERT: D 173 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7151 (ttp80) REVERT: D 175 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: D 189 ASN cc_start: 0.7657 (m-40) cc_final: 0.7323 (m-40) REVERT: D 233 CYS cc_start: 0.6704 (m) cc_final: 0.6430 (m) REVERT: D 330 ASP cc_start: 0.7465 (m-30) cc_final: 0.7131 (m-30) outliers start: 56 outliers final: 23 residues processed: 481 average time/residue: 0.5494 time to fit residues: 291.8403 Evaluate side-chains 460 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 436 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 122 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 149 optimal weight: 0.0770 chunk 56 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 295 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108308 restraints weight = 18357.737| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.55 r_work: 0.3394 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 13766 Z= 0.204 Angle : 0.610 11.146 18744 Z= 0.312 Chirality : 0.048 0.165 2008 Planarity : 0.005 0.042 2393 Dihedral : 5.944 59.545 1918 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.65 % Allowed : 25.25 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.19), residues: 1765 helix: -2.70 (0.50), residues: 52 sheet: 0.60 (0.20), residues: 658 loop : -1.55 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 220 TYR 0.013 0.001 TYR C 253 PHE 0.019 0.002 PHE B 406 TRP 0.016 0.002 TRP D 358 HIS 0.006 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00474 (13735) covalent geometry : angle 0.60469 (18682) SS BOND : bond 0.00554 ( 31) SS BOND : angle 1.46258 ( 62) hydrogen bonds : bond 0.03232 ( 453) hydrogen bonds : angle 6.19638 ( 1188) *********************** 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 482 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 430 time to evaluate : 0.598 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: 0.7846 (tt0) cc_final: 0.7544 (tt0) REVERT: A 369 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8234 (mtpp) REVERT: A 411 GLU cc_start: 0.7820 (mp0) cc_final: 0.7404 (mp0) REVERT: A 453 MET cc_start: 0.8364 (tpp) cc_final: 0.7954 (tpp) REVERT: B 148 THR cc_start: 0.7231 (m) cc_final: 0.7000 (p) REVERT: B 411 GLU cc_start: 0.7332 (mp0) cc_final: 0.6884 (mp0) REVERT: C 175 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7264 (mm-30) REVERT: C 176 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8494 (p) REVERT: C 268 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7211 (tm-30) REVERT: C 273 ASN cc_start: 0.8087 (t0) cc_final: 0.7737 (t0) REVERT: C 316 TYR cc_start: 0.8547 (m-80) cc_final: 0.8334 (m-80) REVERT: C 357 VAL cc_start: 0.8395 (t) cc_final: 0.8137 (p) REVERT: C 411 GLU cc_start: 0.7664 (mp0) cc_final: 0.7352 (mp0) REVERT: C 428 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8189 (mtp180) REVERT: D 173 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7126 (ttp80) REVERT: D 175 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: D 189 ASN cc_start: 0.7665 (m-40) cc_final: 0.7254 (m-40) REVERT: D 213 THR cc_start: 0.8387 (m) cc_final: 0.8077 (p) REVERT: D 330 ASP cc_start: 0.7473 (m-30) cc_final: 0.7131 (m-30) outliers start: 52 outliers final: 36 residues processed: 455 average time/residue: 0.5505 time to fit residues: 276.8128 Evaluate side-chains 460 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 422 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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 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 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 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 7 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 23 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.0040 chunk 157 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 273 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 = 0.3618 r_free = 0.3618 target = 0.116606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108494 restraints weight = 18264.043| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.54 r_work: 0.3398 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 13766 Z= 0.189 Angle : 0.601 11.517 18744 Z= 0.307 Chirality : 0.047 0.162 2008 Planarity : 0.004 0.042 2393 Dihedral : 5.927 59.741 1918 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.14 % Allowed : 24.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.19), residues: 1765 helix: -2.70 (0.50), residues: 52 sheet: 0.60 (0.20), residues: 640 loop : -1.51 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 220 TYR 0.013 0.001 TYR C 253 PHE 0.018 0.002 PHE B 406 TRP 0.016 0.001 TRP D 358 HIS 0.006 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00439 (13735) covalent geometry : angle 0.59649 (18682) SS BOND : bond 0.00563 ( 31) SS BOND : angle 1.41263 ( 62) hydrogen bonds : bond 0.03115 ( 453) hydrogen bonds : angle 6.10967 ( 1188) *********************** 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 493 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 434 time to evaluate : 0.543 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: symmetry clash REVERT: A 277 GLU cc_start: 0.7879 (tt0) cc_final: 0.7577 (tt0) REVERT: A 369 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8235 (mtpp) REVERT: A 411 GLU cc_start: 0.7813 (mp0) cc_final: 0.7397 (mp0) REVERT: A 453 MET cc_start: 0.8369 (tpp) cc_final: 0.7983 (tpp) REVERT: B 107 ARG cc_start: 0.8808 (mtp85) cc_final: 0.8584 (mtp85) REVERT: B 148 THR cc_start: 0.7258 (m) cc_final: 0.7031 (p) REVERT: B 411 GLU cc_start: 0.7303 (mp0) cc_final: 0.6856 (mp0) REVERT: C 175 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7277 (mm-30) REVERT: C 176 SER cc_start: 0.8696 (t) cc_final: 0.8494 (p) REVERT: C 268 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7229 (tm-30) REVERT: C 273 ASN cc_start: 0.8082 (t0) cc_final: 0.7732 (t0) REVERT: C 294 ASP cc_start: 0.7080 (t0) cc_final: 0.6679 (t0) REVERT: C 316 TYR cc_start: 0.8540 (m-80) cc_final: 0.8338 (m-80) REVERT: C 357 VAL cc_start: 0.8398 (t) cc_final: 0.8144 (p) REVERT: C 411 GLU cc_start: 0.7653 (mp0) cc_final: 0.7339 (mp0) REVERT: C 428 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8186 (mtp180) REVERT: D 173 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7137 (ttp80) REVERT: D 175 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: D 189 ASN cc_start: 0.7637 (m-40) cc_final: 0.7276 (m-40) REVERT: D 330 ASP cc_start: 0.7464 (m-30) cc_final: 0.7124 (m-30) outliers start: 59 outliers final: 46 residues processed: 465 average time/residue: 0.5699 time to fit residues: 291.1707 Evaluate side-chains 466 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 419 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 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 367 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain D residue 117 ILE 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 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 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 150 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 0.0170 chunk 67 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 101 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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** B 273 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109432 restraints weight = 18292.153| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.54 r_work: 0.3411 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13766 Z= 0.149 Angle : 0.581 11.715 18744 Z= 0.296 Chirality : 0.046 0.156 2008 Planarity : 0.004 0.041 2393 Dihedral : 5.791 59.409 1918 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.58 % Allowed : 26.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.19), residues: 1765 helix: -2.58 (0.52), residues: 52 sheet: 0.72 (0.20), residues: 642 loop : -1.51 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 220 TYR 0.013 0.001 TYR C 253 PHE 0.016 0.002 PHE B 406 TRP 0.014 0.001 TRP D 358 HIS 0.003 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00348 (13735) covalent geometry : angle 0.57670 (18682) SS BOND : bond 0.00522 ( 31) SS BOND : angle 1.37735 ( 62) hydrogen bonds : bond 0.02941 ( 453) hydrogen bonds : angle 5.98637 ( 1188) *********************** 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 493 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 442 time to evaluate : 0.615 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 277 GLU cc_start: 0.7796 (tt0) cc_final: 0.7530 (tt0) REVERT: A 369 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8248 (mtpp) REVERT: A 411 GLU cc_start: 0.7749 (mp0) cc_final: 0.7370 (mp0) REVERT: A 453 MET cc_start: 0.8293 (tpp) cc_final: 0.7909 (tpp) REVERT: B 148 THR cc_start: 0.7121 (m) cc_final: 0.6900 (p) REVERT: B 411 GLU cc_start: 0.7261 (mp0) cc_final: 0.6834 (mp0) REVERT: C 175 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7256 (mm-30) REVERT: C 268 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7220 (tm-30) REVERT: C 273 ASN cc_start: 0.8025 (t0) cc_final: 0.7693 (t0) REVERT: C 294 ASP cc_start: 0.7104 (t0) cc_final: 0.6712 (t0) REVERT: C 357 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8153 (p) REVERT: C 411 GLU cc_start: 0.7577 (mp0) cc_final: 0.7291 (mp0) REVERT: C 433 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7331 (mt-10) REVERT: D 173 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7154 (ttp80) REVERT: D 175 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: D 189 ASN cc_start: 0.7622 (m-40) cc_final: 0.7284 (m-40) REVERT: D 213 THR cc_start: 0.8348 (m) cc_final: 0.8098 (p) REVERT: D 330 ASP cc_start: 0.7438 (m-30) cc_final: 0.7119 (m-30) REVERT: D 453 MET cc_start: 0.8236 (tpp) cc_final: 0.7949 (tpp) outliers start: 51 outliers final: 35 residues processed: 472 average time/residue: 0.5396 time to fit residues: 281.3335 Evaluate side-chains 467 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 430 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 332 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 C residue 184 CYS Chi-restraints excluded: chain C residue 191 LEU 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 295 ASN Chi-restraints excluded: chain D residue 297 HIS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 439 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 31 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 101 optimal weight: 0.0030 chunk 172 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 0.2980 chunk 52 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 295 ASN A 341 ASN B 378 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN 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 = 0.117578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109435 restraints weight = 18225.366| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.54 r_work: 0.3415 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13766 Z= 0.154 Angle : 0.586 12.066 18744 Z= 0.299 Chirality : 0.047 0.156 2008 Planarity : 0.004 0.041 2393 Dihedral : 5.735 59.717 1917 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.51 % Allowed : 26.65 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.19), residues: 1765 helix: -2.61 (0.51), residues: 52 sheet: 0.61 (0.20), residues: 640 loop : -1.51 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.012 0.001 TYR C 253 PHE 0.016 0.002 PHE B 406 TRP 0.014 0.001 TRP D 358 HIS 0.004 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00360 (13735) covalent geometry : angle 0.58113 (18682) SS BOND : bond 0.00560 ( 31) SS BOND : angle 1.46249 ( 62) hydrogen bonds : bond 0.02949 ( 453) hydrogen bonds : angle 5.96785 ( 1188) *********************** 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 483 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 433 time to evaluate : 0.594 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: symmetry clash REVERT: A 273 ASN cc_start: 0.7772 (t0) cc_final: 0.7561 (t0) REVERT: A 277 GLU cc_start: 0.7852 (tt0) cc_final: 0.7551 (tt0) REVERT: A 411 GLU cc_start: 0.7810 (mp0) cc_final: 0.7401 (mp0) REVERT: A 453 MET cc_start: 0.8336 (tpp) cc_final: 0.7951 (tpp) REVERT: B 148 THR cc_start: 0.7116 (m) cc_final: 0.6890 (p) REVERT: B 411 GLU cc_start: 0.7313 (mp0) cc_final: 0.6869 (mp0) REVERT: C 175 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7289 (mm-30) REVERT: C 268 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7211 (tm-30) REVERT: C 273 ASN cc_start: 0.8071 (t0) cc_final: 0.7723 (t0) REVERT: C 357 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8152 (p) REVERT: C 411 GLU cc_start: 0.7631 (mp0) cc_final: 0.7328 (mp0) REVERT: D 173 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7148 (ttp80) REVERT: D 175 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: D 189 ASN cc_start: 0.7653 (m-40) cc_final: 0.7288 (m-40) REVERT: D 213 THR cc_start: 0.8370 (m) cc_final: 0.8082 (p) REVERT: D 330 ASP cc_start: 0.7454 (m-30) cc_final: 0.7125 (m-30) REVERT: D 453 MET cc_start: 0.8278 (tpp) cc_final: 0.7968 (tpp) outliers start: 50 outliers final: 42 residues processed: 458 average time/residue: 0.5350 time to fit residues: 271.3445 Evaluate side-chains 469 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 425 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 B residue 240 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL 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 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 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 21 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109016 restraints weight = 18203.314| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.55 r_work: 0.3407 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13766 Z= 0.179 Angle : 0.606 12.977 18744 Z= 0.309 Chirality : 0.047 0.179 2008 Planarity : 0.004 0.041 2393 Dihedral : 5.810 59.910 1917 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.51 % Allowed : 26.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.19), residues: 1765 helix: -2.67 (0.50), residues: 52 sheet: 0.64 (0.20), residues: 630 loop : -1.51 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 220 TYR 0.014 0.001 TYR A 274 PHE 0.017 0.002 PHE B 406 TRP 0.015 0.001 TRP D 358 HIS 0.004 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00418 (13735) covalent geometry : angle 0.60075 (18682) SS BOND : bond 0.00600 ( 31) SS BOND : angle 1.56375 ( 62) hydrogen bonds : bond 0.03047 ( 453) hydrogen bonds : angle 6.01154 ( 1188) *********************** 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 486 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 436 time to evaluate : 0.550 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: symmetry clash REVERT: A 277 GLU cc_start: 0.7849 (tt0) cc_final: 0.7550 (tt0) REVERT: A 411 GLU cc_start: 0.7804 (mp0) cc_final: 0.7388 (mp0) REVERT: A 453 MET cc_start: 0.8333 (tpp) cc_final: 0.7949 (tpp) REVERT: B 131 THR cc_start: 0.8258 (m) cc_final: 0.7990 (m) REVERT: B 148 THR cc_start: 0.7158 (m) cc_final: 0.6931 (p) REVERT: B 411 GLU cc_start: 0.7312 (mp0) cc_final: 0.6867 (mp0) REVERT: C 175 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7297 (mm-30) REVERT: C 268 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7215 (tm-30) REVERT: C 273 ASN cc_start: 0.8055 (t0) cc_final: 0.7706 (t0) REVERT: C 357 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8140 (p) REVERT: C 411 GLU cc_start: 0.7637 (mp0) cc_final: 0.7334 (mp0) REVERT: D 173 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7153 (ttp80) REVERT: D 175 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: D 189 ASN cc_start: 0.7658 (m-40) cc_final: 0.7293 (m-40) REVERT: D 330 ASP cc_start: 0.7456 (m-30) cc_final: 0.7123 (m-30) outliers start: 50 outliers final: 42 residues processed: 463 average time/residue: 0.5491 time to fit residues: 280.1629 Evaluate side-chains 458 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 414 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 378 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 131 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.0000 chunk 172 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 B 378 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108901 restraints weight = 18105.902| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.53 r_work: 0.3405 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13766 Z= 0.181 Angle : 0.611 13.179 18744 Z= 0.311 Chirality : 0.047 0.191 2008 Planarity : 0.004 0.041 2393 Dihedral : 5.832 59.655 1917 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.79 % Allowed : 27.00 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.19), residues: 1765 helix: -2.67 (0.50), residues: 52 sheet: 0.57 (0.20), residues: 654 loop : -1.53 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 220 TYR 0.014 0.001 TYR C 253 PHE 0.017 0.002 PHE B 406 TRP 0.018 0.001 TRP A 219 HIS 0.004 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00423 (13735) covalent geometry : angle 0.60516 (18682) SS BOND : bond 0.00601 ( 31) SS BOND : angle 1.59455 ( 62) hydrogen bonds : bond 0.03059 ( 453) hydrogen bonds : angle 6.01969 ( 1188) *********************** 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 485 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 431 time to evaluate : 0.557 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: symmetry clash REVERT: A 277 GLU cc_start: 0.7861 (tt0) cc_final: 0.7576 (tt0) REVERT: A 411 GLU cc_start: 0.7798 (mp0) cc_final: 0.7377 (mp0) REVERT: A 453 MET cc_start: 0.8338 (tpp) cc_final: 0.7952 (tpp) REVERT: B 148 THR cc_start: 0.7208 (m) cc_final: 0.6983 (p) REVERT: B 378 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6636 (p0) REVERT: B 411 GLU cc_start: 0.7318 (mp0) cc_final: 0.6876 (mp0) REVERT: C 175 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7299 (mm-30) REVERT: C 268 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7218 (tm-30) REVERT: C 273 ASN cc_start: 0.8042 (t0) cc_final: 0.7698 (t0) REVERT: C 294 ASP cc_start: 0.7040 (t0) cc_final: 0.6673 (t0) REVERT: C 316 TYR cc_start: 0.8556 (m-80) cc_final: 0.8339 (m-80) REVERT: C 357 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8143 (p) REVERT: C 411 GLU cc_start: 0.7640 (mp0) cc_final: 0.7335 (mp0) REVERT: D 173 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7141 (ttp80) REVERT: D 175 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: D 189 ASN cc_start: 0.7666 (m-40) cc_final: 0.7285 (m-40) REVERT: D 213 THR cc_start: 0.8361 (m) cc_final: 0.8086 (p) REVERT: D 330 ASP cc_start: 0.7451 (m-30) cc_final: 0.7122 (m-30) outliers start: 54 outliers final: 45 residues processed: 461 average time/residue: 0.5432 time to fit residues: 276.0061 Evaluate side-chains 462 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 414 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 378 ASN 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 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 297 HIS 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 22 THR Chi-restraints excluded: chain L residue 31 THR 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 101 optimal weight: 0.0170 chunk 134 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 151 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.117243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109106 restraints weight = 18292.831| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.55 r_work: 0.3408 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1082 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= 0.173 Angle : 0.611 13.001 18744 Z= 0.311 Chirality : 0.047 0.187 2008 Planarity : 0.004 0.045 2393 Dihedral : 5.828 59.504 1917 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.65 % Allowed : 27.07 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 1765 helix: -2.66 (0.50), residues: 52 sheet: 0.64 (0.21), residues: 630 loop : -1.50 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 220 TYR 0.017 0.001 TYR A 274 PHE 0.017 0.002 PHE B 406 TRP 0.016 0.001 TRP A 219 HIS 0.004 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00405 (13735) covalent geometry : angle 0.60584 (18682) SS BOND : bond 0.00597 ( 31) SS BOND : angle 1.53383 ( 62) hydrogen bonds : bond 0.03032 ( 453) hydrogen bonds : angle 6.01423 ( 1188) *********************** 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 472 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 420 time to evaluate : 0.562 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: symmetry clash REVERT: A 277 GLU cc_start: 0.7849 (tt0) cc_final: 0.7575 (tt0) REVERT: A 411 GLU cc_start: 0.7784 (mp0) cc_final: 0.7369 (mp0) REVERT: A 438 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8384 (p) REVERT: A 453 MET cc_start: 0.8341 (tpp) cc_final: 0.7958 (tpp) REVERT: B 148 THR cc_start: 0.7195 (m) cc_final: 0.6966 (p) REVERT: B 411 GLU cc_start: 0.7310 (mp0) cc_final: 0.6866 (mp0) REVERT: C 175 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7303 (mm-30) REVERT: C 268 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7217 (tm-30) REVERT: C 273 ASN cc_start: 0.8045 (t0) cc_final: 0.7685 (t0) REVERT: C 294 ASP cc_start: 0.7041 (t0) cc_final: 0.6650 (t0) REVERT: C 316 TYR cc_start: 0.8558 (m-80) cc_final: 0.8323 (m-80) REVERT: C 357 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8139 (p) REVERT: C 411 GLU cc_start: 0.7634 (mp0) cc_final: 0.7339 (mp0) REVERT: D 175 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: D 189 ASN cc_start: 0.7642 (m-40) cc_final: 0.7278 (m-40) REVERT: D 213 THR cc_start: 0.8376 (m) cc_final: 0.8085 (p) REVERT: D 330 ASP cc_start: 0.7449 (m-30) cc_final: 0.7123 (m-30) outliers start: 52 outliers final: 45 residues processed: 451 average time/residue: 0.5177 time to fit residues: 258.3991 Evaluate side-chains 469 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 421 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 266 SER Chi-restraints excluded: chain B residue 378 ASN 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 297 HIS 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 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 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 136 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN B 378 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 = 0.3618 r_free = 0.3618 target = 0.116413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108267 restraints weight = 18086.744| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.53 r_work: 0.3401 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 13766 Z= 0.236 Angle : 0.649 13.575 18744 Z= 0.331 Chirality : 0.049 0.205 2008 Planarity : 0.004 0.046 2393 Dihedral : 6.017 59.038 1917 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.44 % Allowed : 27.49 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.19), residues: 1765 helix: -2.86 (0.46), residues: 52 sheet: 0.60 (0.21), residues: 630 loop : -1.53 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 220 TYR 0.016 0.001 TYR C 253 PHE 0.021 0.002 PHE B 406 TRP 0.017 0.002 TRP D 358 HIS 0.006 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00549 (13735) covalent geometry : angle 0.64347 (18682) SS BOND : bond 0.00670 ( 31) SS BOND : angle 1.64820 ( 62) hydrogen bonds : bond 0.03286 ( 453) hydrogen bonds : angle 6.13568 ( 1188) ********************** 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 467 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 418 time to evaluate : 0.532 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: 0.7849 (tt0) cc_final: 0.7557 (tt0) REVERT: A 373 MET cc_start: 0.8198 (mmm) cc_final: 0.7867 (mmm) REVERT: A 438 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8377 (p) REVERT: A 453 MET cc_start: 0.8377 (tpp) cc_final: 0.7997 (tpp) REVERT: B 148 THR cc_start: 0.7329 (m) cc_final: 0.7077 (p) REVERT: B 411 GLU cc_start: 0.7326 (mp0) cc_final: 0.6881 (mp0) REVERT: C 156 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7383 (mtt180) REVERT: C 175 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7273 (mm-30) REVERT: C 268 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7203 (tm-30) REVERT: C 273 ASN cc_start: 0.8047 (t0) cc_final: 0.7699 (t0) REVERT: C 294 ASP cc_start: 0.7075 (t0) cc_final: 0.6704 (t0) REVERT: C 316 TYR cc_start: 0.8587 (m-80) cc_final: 0.8381 (m-80) REVERT: C 357 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8153 (p) REVERT: C 411 GLU cc_start: 0.7681 (mp0) cc_final: 0.7372 (mp0) REVERT: D 175 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: D 189 ASN cc_start: 0.7661 (m-40) cc_final: 0.7299 (m-40) REVERT: D 213 THR cc_start: 0.8362 (m) cc_final: 0.8060 (p) REVERT: D 330 ASP cc_start: 0.7435 (m-30) cc_final: 0.7107 (m-30) outliers start: 49 outliers final: 43 residues processed: 447 average time/residue: 0.5084 time to fit residues: 252.4807 Evaluate side-chains 461 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 414 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 266 SER Chi-restraints excluded: chain B residue 378 ASN 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 297 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 165 optimal weight: 0.0060 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 130 optimal weight: 0.0770 chunk 85 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 24 optimal weight: 0.0040 chunk 25 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 overall best weight: 0.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.119147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111040 restraints weight = 18321.014| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.56 r_work: 0.3439 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13766 Z= 0.108 Angle : 0.571 12.040 18744 Z= 0.292 Chirality : 0.046 0.154 2008 Planarity : 0.004 0.041 2393 Dihedral : 5.595 59.305 1917 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.52 % Allowed : 28.47 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.19), residues: 1765 helix: -2.49 (0.54), residues: 52 sheet: 0.69 (0.21), residues: 624 loop : -1.48 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 220 TYR 0.016 0.001 TYR A 274 PHE 0.012 0.001 PHE C 121 TRP 0.022 0.001 TRP B 380 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00258 (13735) covalent geometry : angle 0.56651 (18682) SS BOND : bond 0.00499 ( 31) SS BOND : angle 1.30718 ( 62) hydrogen bonds : bond 0.02709 ( 453) hydrogen bonds : angle 5.86385 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7136.36 seconds wall clock time: 122 minutes 26.10 seconds (7346.10 seconds total)