Starting phenix.real_space_refine on Fri Mar 6 14:04:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nzz_0563/03_2026/6nzz_0563_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nzz_0563/03_2026/6nzz_0563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nzz_0563/03_2026/6nzz_0563_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nzz_0563/03_2026/6nzz_0563_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nzz_0563/03_2026/6nzz_0563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nzz_0563/03_2026/6nzz_0563.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 10390 2.51 5 N 2466 2.21 5 O 2698 1.98 5 H 15330 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30988 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "B" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "C" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "D" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "E" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "F" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'L9Y': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 5.31, per 1000 atoms: 0.17 Number of scatterers: 30988 At special positions: 0 Unit cell: (112.064, 107.712, 127.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2698 8.00 N 2466 7.00 C 10390 6.00 H 15330 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 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: 1.98 Conformation dependent library (CDL) restraints added in 679.0 milliseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 6 sheets defined 70.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 23 through 48 removed outlier: 3.531A pdb=" N PHE A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 39 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 removed outlier: 3.648A pdb=" N TYR A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 143 removed outlier: 3.664A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 3.593A pdb=" N LEU A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.662A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.895A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 removed outlier: 3.579A pdb=" N LEU A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 283 removed outlier: 3.502A pdb=" N MET A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 314 through 346 removed outlier: 3.745A pdb=" N SER A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 340 " --> pdb=" O CYS A 336 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 4.516A pdb=" N SER A 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 372 through 383 removed outlier: 4.030A pdb=" N ILE A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.244A pdb=" N LYS A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 404 Processing helix chain 'B' and resid 23 through 48 removed outlier: 3.532A pdb=" N PHE B 27 " --> pdb=" O TRP B 23 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 39 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.648A pdb=" N TYR B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 143 removed outlier: 3.664A pdb=" N LYS B 123 " --> pdb=" O HIS B 119 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 3.592A pdb=" N LEU B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 4.661A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.894A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 255 removed outlier: 3.580A pdb=" N LEU B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 254 " --> pdb=" O PHE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 283 removed outlier: 3.502A pdb=" N MET B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.745A pdb=" N SER B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 340 " --> pdb=" O CYS B 336 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 4.516A pdb=" N SER B 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 372 through 383 removed outlier: 4.030A pdb=" N ILE B 379 " --> pdb=" O MET B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.245A pdb=" N LYS B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 390 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 404 Processing helix chain 'C' and resid 23 through 48 removed outlier: 3.532A pdb=" N PHE C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 39 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY C 42 " --> pdb=" O ILE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.648A pdb=" N TYR C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 143 removed outlier: 3.665A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 3.592A pdb=" N LEU C 130 " --> pdb=" O PRO C 126 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.662A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.895A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 255 removed outlier: 3.579A pdb=" N LEU C 243 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 283 removed outlier: 3.502A pdb=" N MET C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 314 through 346 removed outlier: 3.745A pdb=" N SER C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR C 332 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 340 " --> pdb=" O CYS C 336 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 346 " --> pdb=" O TRP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 355 removed outlier: 4.515A pdb=" N SER C 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 355' Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 372 through 383 removed outlier: 4.030A pdb=" N ILE C 379 " --> pdb=" O MET C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 4.244A pdb=" N LYS C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 390 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 404 Processing helix chain 'D' and resid 23 through 48 removed outlier: 3.531A pdb=" N PHE D 27 " --> pdb=" O TRP D 23 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 39 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.648A pdb=" N TYR D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 143 removed outlier: 3.664A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 3.592A pdb=" N LEU D 130 " --> pdb=" O PRO D 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 4.661A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.896A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 255 removed outlier: 3.579A pdb=" N LEU D 243 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 254 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 283 removed outlier: 3.501A pdb=" N MET D 265 " --> pdb=" O TYR D 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 289 Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.745A pdb=" N SER D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 340 " --> pdb=" O CYS D 336 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 355 removed outlier: 4.516A pdb=" N SER D 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 352 through 355' Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 372 through 383 removed outlier: 4.029A pdb=" N ILE D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 4.245A pdb=" N LYS D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 390 " --> pdb=" O TYR D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 404 Processing helix chain 'E' and resid 23 through 48 removed outlier: 3.532A pdb=" N PHE E 27 " --> pdb=" O TRP E 23 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 39 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY E 42 " --> pdb=" O ILE E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 116 removed outlier: 3.648A pdb=" N TYR E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 143 removed outlier: 3.664A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 3.592A pdb=" N LEU E 130 " --> pdb=" O PRO E 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 4.662A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 174 removed outlier: 3.894A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 255 removed outlier: 3.579A pdb=" N LEU E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 254 " --> pdb=" O PHE E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 283 removed outlier: 3.502A pdb=" N MET E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL E 272 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE E 273 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE E 275 " --> pdb=" O LYS E 271 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 314 through 346 removed outlier: 3.745A pdb=" N SER E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 340 " --> pdb=" O CYS E 336 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG E 346 " --> pdb=" O TRP E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 355 removed outlier: 4.515A pdb=" N SER E 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 352 through 355' Processing helix chain 'E' and resid 356 through 361 Processing helix chain 'E' and resid 372 through 383 removed outlier: 4.030A pdb=" N ILE E 379 " --> pdb=" O MET E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 390 removed outlier: 4.244A pdb=" N LYS E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 390 " --> pdb=" O TYR E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 404 Processing helix chain 'F' and resid 23 through 48 removed outlier: 3.531A pdb=" N PHE F 27 " --> pdb=" O TRP F 23 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 39 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 42 " --> pdb=" O ILE F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.648A pdb=" N TYR F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 143 removed outlier: 3.665A pdb=" N LYS F 123 " --> pdb=" O HIS F 119 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 3.592A pdb=" N LEU F 130 " --> pdb=" O PRO F 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER F 140 " --> pdb=" O PHE F 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.662A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.894A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 255 removed outlier: 3.579A pdb=" N LEU F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL F 254 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 283 removed outlier: 3.503A pdb=" N MET F 265 " --> pdb=" O TYR F 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE F 273 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 289 Processing helix chain 'F' and resid 314 through 346 removed outlier: 3.746A pdb=" N SER F 327 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 338 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 340 " --> pdb=" O CYS F 336 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG F 346 " --> pdb=" O TRP F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 355 removed outlier: 4.516A pdb=" N SER F 355 " --> pdb=" O SER F 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 352 through 355' Processing helix chain 'F' and resid 356 through 361 Processing helix chain 'F' and resid 372 through 383 removed outlier: 4.030A pdb=" N ILE F 379 " --> pdb=" O MET F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 390 removed outlier: 4.245A pdb=" N LYS F 388 " --> pdb=" O PRO F 384 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE F 390 " --> pdb=" O TYR F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 404 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 762 hydrogen bonds defined for protein. 2232 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: 7.00 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15306 1.03 - 1.22: 42 1.22 - 1.42: 7002 1.42 - 1.61: 8924 1.61 - 1.81: 148 Bond restraints: 31422 Sorted by residual: bond pdb=" C31 POV E 901 " pdb=" O32 POV E 901 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C31 POV B 901 " pdb=" O32 POV B 901 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C31 POV A 901 " pdb=" O32 POV A 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C31 POV D 901 " pdb=" O32 POV D 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C31 POV C 901 " pdb=" O32 POV C 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 31417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 55897 2.84 - 5.67: 500 5.67 - 8.51: 48 8.51 - 11.34: 9 11.34 - 14.18: 7 Bond angle restraints: 56461 Sorted by residual: angle pdb=" C32 POV E 901 " pdb=" C31 POV E 901 " pdb=" O31 POV E 901 " ideal model delta sigma weight residual 110.66 124.84 -14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C32 POV A 901 " pdb=" C31 POV A 901 " pdb=" O31 POV A 901 " ideal model delta sigma weight residual 110.66 124.80 -14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C32 POV F 901 " pdb=" C31 POV F 901 " pdb=" O31 POV F 901 " ideal model delta sigma weight residual 110.66 124.79 -14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C32 POV B 901 " pdb=" C31 POV B 901 " pdb=" O31 POV B 901 " ideal model delta sigma weight residual 110.66 124.78 -14.12 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C32 POV D 901 " pdb=" C31 POV D 901 " pdb=" O31 POV D 901 " ideal model delta sigma weight residual 110.66 124.76 -14.10 3.00e+00 1.11e-01 2.21e+01 ... (remaining 56456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 13190 17.43 - 34.86: 1359 34.86 - 52.28: 314 52.28 - 69.71: 85 69.71 - 87.14: 14 Dihedral angle restraints: 14962 sinusoidal: 7816 harmonic: 7146 Sorted by residual: dihedral pdb=" CA THR B 296 " pdb=" C THR B 296 " pdb=" N VAL B 297 " pdb=" CA VAL B 297 " ideal model delta harmonic sigma weight residual -180.00 -158.82 -21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA THR E 296 " pdb=" C THR E 296 " pdb=" N VAL E 297 " pdb=" CA VAL E 297 " ideal model delta harmonic sigma weight residual 180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA THR C 296 " pdb=" C THR C 296 " pdb=" N VAL C 297 " pdb=" CA VAL C 297 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 14959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2045 0.060 - 0.120: 283 0.120 - 0.180: 25 0.180 - 0.240: 0 0.240 - 0.300: 1 Chirality restraints: 2354 Sorted by residual: chirality pdb=" C24 L9Y F 904 " pdb=" C05 L9Y F 904 " pdb=" C25 L9Y F 904 " pdb=" C28 L9Y F 904 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C05 L9Y F 904 " pdb=" C06 L9Y F 904 " pdb=" C09 L9Y F 904 " pdb=" C24 L9Y F 904 " both_signs ideal model delta sigma weight residual False 2.95 3.12 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CG LEU B 376 " pdb=" CB LEU B 376 " pdb=" CD1 LEU B 376 " pdb=" CD2 LEU B 376 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2351 not shown) Planarity restraints: 4377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 166 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 167 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 166 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO F 167 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 166 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO D 167 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " -0.022 5.00e-02 4.00e+02 ... (remaining 4374 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 4953 2.28 - 2.86: 68125 2.86 - 3.44: 77267 3.44 - 4.02: 101627 4.02 - 4.60: 157226 Nonbonded interactions: 409198 Sorted by model distance: nonbonded pdb=" O PHE E 164 " pdb="HH11 ARG E 389 " model vdw 1.701 2.450 nonbonded pdb=" O PHE C 164 " pdb="HH11 ARG C 389 " model vdw 1.701 2.450 nonbonded pdb=" O PHE D 164 " pdb="HH11 ARG D 389 " model vdw 1.701 2.450 nonbonded pdb=" O PHE B 164 " pdb="HH11 ARG B 389 " model vdw 1.702 2.450 nonbonded pdb=" O PHE A 164 " pdb="HH11 ARG A 389 " model vdw 1.702 2.450 ... (remaining 409193 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 15 through 903) } 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.420 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.007 0.151 16110 Z= 0.307 Angle : 0.941 14.178 21763 Z= 0.466 Chirality : 0.042 0.300 2354 Planarity : 0.004 0.040 2613 Dihedral : 14.226 71.524 5878 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.17 % Allowed : 13.38 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.16), residues: 1800 helix: -3.61 (0.10), residues: 1152 sheet: -0.43 (0.46), residues: 96 loop : -2.08 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 251 TYR 0.014 0.002 TYR A 281 PHE 0.022 0.002 PHE A 125 TRP 0.020 0.002 TRP D 143 HIS 0.009 0.002 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00664 (16092) covalent geometry : angle 0.94204 (21727) SS BOND : bond 0.00082 ( 18) SS BOND : angle 0.48120 ( 36) hydrogen bonds : bond 0.29051 ( 762) hydrogen bonds : angle 9.88592 ( 2232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 0.725 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: 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: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.7157 (OUTLIER) cc_final: 0.6807 (m) REVERT: A 140 SER cc_start: 0.7404 (t) cc_final: 0.7181 (p) REVERT: A 145 LYS cc_start: 0.7684 (mmtt) cc_final: 0.6860 (ttpt) REVERT: A 279 ILE cc_start: 0.6695 (mm) cc_final: 0.6346 (pt) REVERT: A 286 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7402 (t) REVERT: A 335 ILE cc_start: 0.5602 (OUTLIER) cc_final: 0.5199 (mt) REVERT: A 358 GLU cc_start: 0.5873 (tt0) cc_final: 0.5624 (mm-30) REVERT: B 28 THR cc_start: 0.7243 (OUTLIER) cc_final: 0.6920 (m) REVERT: B 124 TYR cc_start: 0.8022 (m-10) cc_final: 0.7757 (m-10) REVERT: B 140 SER cc_start: 0.7962 (t) cc_final: 0.7626 (p) REVERT: B 145 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7076 (ttpt) REVERT: B 149 THR cc_start: 0.7611 (p) cc_final: 0.7383 (t) REVERT: B 279 ILE cc_start: 0.6701 (mm) cc_final: 0.6389 (pt) REVERT: B 329 VAL cc_start: 0.6895 (OUTLIER) cc_final: 0.6454 (t) REVERT: B 335 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5452 (mt) REVERT: B 376 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5769 (tp) REVERT: C 28 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6824 (m) REVERT: C 145 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7071 (ttpp) REVERT: C 279 ILE cc_start: 0.6458 (mm) cc_final: 0.6135 (pt) REVERT: C 286 VAL cc_start: 0.7573 (OUTLIER) cc_final: 0.7165 (t) REVERT: C 335 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5308 (mt) REVERT: D 28 THR cc_start: 0.7186 (OUTLIER) cc_final: 0.6744 (m) REVERT: D 140 SER cc_start: 0.7148 (t) cc_final: 0.6937 (p) REVERT: D 145 LYS cc_start: 0.7608 (mmtt) cc_final: 0.6807 (ttpt) REVERT: D 265 MET cc_start: 0.6606 (tpt) cc_final: 0.6387 (tpt) REVERT: D 279 ILE cc_start: 0.6812 (mm) cc_final: 0.6468 (pt) REVERT: D 286 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7349 (t) REVERT: D 335 ILE cc_start: 0.5654 (OUTLIER) cc_final: 0.5308 (mt) REVERT: E 28 THR cc_start: 0.6945 (OUTLIER) cc_final: 0.6262 (p) REVERT: E 50 ASP cc_start: 0.8075 (t70) cc_final: 0.7779 (t70) REVERT: E 140 SER cc_start: 0.7737 (t) cc_final: 0.7458 (p) REVERT: E 149 THR cc_start: 0.7516 (p) cc_final: 0.7098 (t) REVERT: E 329 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6527 (t) REVERT: E 335 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5583 (mt) REVERT: E 358 GLU cc_start: 0.5869 (tt0) cc_final: 0.5067 (mp0) REVERT: F 28 THR cc_start: 0.7148 (OUTLIER) cc_final: 0.6775 (m) REVERT: F 145 LYS cc_start: 0.7699 (mmtt) cc_final: 0.6884 (ttpt) REVERT: F 279 ILE cc_start: 0.6713 (mm) cc_final: 0.6331 (pt) REVERT: F 286 VAL cc_start: 0.7590 (OUTLIER) cc_final: 0.7243 (t) REVERT: F 335 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5589 (mt) REVERT: F 376 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5655 (tp) outliers start: 54 outliers final: 9 residues processed: 300 average time/residue: 0.2088 time to fit residues: 100.3960 Evaluate side-chains 211 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A 132 HIS A 155 HIS A 267 GLN B 104 HIS B 132 HIS B 155 HIS B 267 GLN C 104 HIS C 155 HIS C 267 GLN D 104 HIS D 267 GLN E 132 HIS E 155 HIS E 267 GLN F 132 HIS F 155 HIS F 267 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.207876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.163748 restraints weight = 55392.132| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.96 r_work: 0.4016 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16110 Z= 0.168 Angle : 0.601 5.256 21763 Z= 0.337 Chirality : 0.038 0.128 2354 Planarity : 0.005 0.052 2613 Dihedral : 9.357 59.678 2268 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.52 % Allowed : 17.25 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.17), residues: 1800 helix: -2.21 (0.12), residues: 1152 sheet: -0.47 (0.42), residues: 96 loop : -2.04 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 309 TYR 0.014 0.001 TYR B 332 PHE 0.020 0.002 PHE D 331 TRP 0.015 0.001 TRP E 143 HIS 0.009 0.002 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00367 (16092) covalent geometry : angle 0.60127 (21727) SS BOND : bond 0.00212 ( 18) SS BOND : angle 0.34126 ( 36) hydrogen bonds : bond 0.06671 ( 762) hydrogen bonds : angle 5.54101 ( 2232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.739 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.7880 (tp30) cc_final: 0.7303 (tp30) REVERT: A 140 SER cc_start: 0.7903 (t) cc_final: 0.7365 (p) REVERT: A 145 LYS cc_start: 0.7488 (mmtt) cc_final: 0.6360 (ttpt) REVERT: A 279 ILE cc_start: 0.7326 (mm) cc_final: 0.6507 (pt) REVERT: A 284 TYR cc_start: 0.7561 (t80) cc_final: 0.7319 (t80) REVERT: A 307 THR cc_start: 0.9057 (p) cc_final: 0.8688 (t) REVERT: A 358 GLU cc_start: 0.5398 (tt0) cc_final: 0.5047 (tp30) REVERT: A 377 HIS cc_start: 0.6632 (OUTLIER) cc_final: 0.6104 (t-170) REVERT: B 50 ASP cc_start: 0.8248 (t70) cc_final: 0.7864 (t70) REVERT: B 115 GLU cc_start: 0.8153 (tp30) cc_final: 0.7538 (tp30) REVERT: B 140 SER cc_start: 0.8098 (t) cc_final: 0.7547 (p) REVERT: B 145 LYS cc_start: 0.7785 (mmtt) cc_final: 0.6712 (ttpt) REVERT: B 279 ILE cc_start: 0.7185 (mm) cc_final: 0.6513 (pt) REVERT: B 307 THR cc_start: 0.8963 (p) cc_final: 0.8678 (t) REVERT: B 329 VAL cc_start: 0.6582 (OUTLIER) cc_final: 0.6117 (t) REVERT: B 375 MET cc_start: 0.7639 (mtm) cc_final: 0.7348 (mtp) REVERT: B 377 HIS cc_start: 0.6677 (OUTLIER) cc_final: 0.6149 (t-170) REVERT: C 145 LYS cc_start: 0.7454 (mmtt) cc_final: 0.6513 (ttpp) REVERT: C 279 ILE cc_start: 0.7036 (mm) cc_final: 0.6353 (pt) REVERT: C 284 TYR cc_start: 0.7320 (t80) cc_final: 0.7115 (t80) REVERT: C 286 VAL cc_start: 0.7355 (OUTLIER) cc_final: 0.6979 (t) REVERT: C 377 HIS cc_start: 0.6776 (OUTLIER) cc_final: 0.6125 (t-170) REVERT: D 115 GLU cc_start: 0.7806 (tp30) cc_final: 0.7121 (tp30) REVERT: D 133 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7802 (t) REVERT: D 140 SER cc_start: 0.7631 (t) cc_final: 0.7138 (p) REVERT: D 145 LYS cc_start: 0.7455 (mmtt) cc_final: 0.6260 (ttpt) REVERT: D 255 GLU cc_start: 0.6330 (mt-10) cc_final: 0.6089 (pt0) REVERT: D 279 ILE cc_start: 0.7230 (mm) cc_final: 0.6345 (pt) REVERT: D 284 TYR cc_start: 0.7612 (t80) cc_final: 0.7305 (t80) REVERT: E 50 ASP cc_start: 0.8509 (t70) cc_final: 0.7936 (t70) REVERT: E 115 GLU cc_start: 0.8048 (tp30) cc_final: 0.7591 (tp30) REVERT: E 129 VAL cc_start: 0.8058 (m) cc_final: 0.7834 (m) REVERT: E 133 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7595 (t) REVERT: E 140 SER cc_start: 0.8094 (t) cc_final: 0.7554 (p) REVERT: E 329 VAL cc_start: 0.6473 (OUTLIER) cc_final: 0.6074 (t) REVERT: E 377 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.6038 (t-170) REVERT: F 145 LYS cc_start: 0.7826 (mmtt) cc_final: 0.6686 (ttpp) REVERT: F 279 ILE cc_start: 0.7358 (mm) cc_final: 0.6537 (pt) REVERT: F 286 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7101 (t) outliers start: 43 outliers final: 17 residues processed: 262 average time/residue: 0.2466 time to fit residues: 97.2035 Evaluate side-chains 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 108 optimal weight: 0.3980 chunk 135 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 0.0170 chunk 173 optimal weight: 1.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.201565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.161612 restraints weight = 52415.488| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 2.61 r_work: 0.4008 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16110 Z= 0.134 Angle : 0.525 4.329 21763 Z= 0.295 Chirality : 0.037 0.125 2354 Planarity : 0.004 0.040 2613 Dihedral : 8.207 59.828 2243 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.11 % Allowed : 19.42 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.18), residues: 1800 helix: -1.21 (0.13), residues: 1194 sheet: 0.07 (0.43), residues: 96 loop : -1.96 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 389 TYR 0.011 0.001 TYR B 332 PHE 0.015 0.001 PHE D 331 TRP 0.013 0.001 TRP C 143 HIS 0.008 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00296 (16092) covalent geometry : angle 0.52522 (21727) SS BOND : bond 0.00194 ( 18) SS BOND : angle 0.27915 ( 36) hydrogen bonds : bond 0.05122 ( 762) hydrogen bonds : angle 4.69159 ( 2232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.776 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8262 (tp30) cc_final: 0.7592 (tp30) REVERT: A 133 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7909 (t) REVERT: A 140 SER cc_start: 0.7975 (t) cc_final: 0.7411 (p) REVERT: A 265 MET cc_start: 0.6747 (tpt) cc_final: 0.6476 (tpt) REVERT: A 274 LYS cc_start: 0.7399 (mtpp) cc_final: 0.7139 (mtpt) REVERT: A 279 ILE cc_start: 0.7412 (mm) cc_final: 0.6530 (pt) REVERT: A 284 TYR cc_start: 0.7760 (t80) cc_final: 0.7466 (t80) REVERT: A 307 THR cc_start: 0.9128 (p) cc_final: 0.8776 (t) REVERT: A 358 GLU cc_start: 0.5506 (tt0) cc_final: 0.5214 (tp30) REVERT: A 377 HIS cc_start: 0.6624 (OUTLIER) cc_final: 0.6035 (t-170) REVERT: B 115 GLU cc_start: 0.8306 (tp30) cc_final: 0.7690 (tp30) REVERT: B 140 SER cc_start: 0.8066 (t) cc_final: 0.7498 (p) REVERT: B 279 ILE cc_start: 0.7205 (mm) cc_final: 0.6473 (pt) REVERT: B 307 THR cc_start: 0.9023 (p) cc_final: 0.8708 (t) REVERT: B 329 VAL cc_start: 0.6691 (OUTLIER) cc_final: 0.6294 (t) REVERT: B 331 PHE cc_start: 0.7001 (t80) cc_final: 0.6357 (m-10) REVERT: B 337 MET cc_start: 0.5947 (ppp) cc_final: 0.5497 (ppp) REVERT: B 377 HIS cc_start: 0.6608 (OUTLIER) cc_final: 0.6064 (t-170) REVERT: C 265 MET cc_start: 0.6363 (tpt) cc_final: 0.6127 (tpt) REVERT: C 279 ILE cc_start: 0.7096 (mm) cc_final: 0.6318 (pt) REVERT: C 284 TYR cc_start: 0.7536 (t80) cc_final: 0.7279 (t80) REVERT: C 286 VAL cc_start: 0.7401 (OUTLIER) cc_final: 0.6971 (t) REVERT: C 309 ARG cc_start: 0.8118 (tpt-90) cc_final: 0.7853 (mmm-85) REVERT: C 331 PHE cc_start: 0.6636 (t80) cc_final: 0.6170 (m-10) REVERT: C 375 MET cc_start: 0.7248 (mtm) cc_final: 0.6942 (mtp) REVERT: C 377 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.6049 (t-170) REVERT: D 115 GLU cc_start: 0.8214 (tp30) cc_final: 0.7450 (tp30) REVERT: D 140 SER cc_start: 0.7751 (t) cc_final: 0.7232 (p) REVERT: D 145 LYS cc_start: 0.7393 (mmtt) cc_final: 0.6203 (ttpt) REVERT: D 255 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6131 (pt0) REVERT: D 279 ILE cc_start: 0.7458 (mm) cc_final: 0.6588 (pt) REVERT: E 50 ASP cc_start: 0.8596 (t70) cc_final: 0.8062 (t70) REVERT: E 140 SER cc_start: 0.8112 (t) cc_final: 0.7579 (p) REVERT: E 329 VAL cc_start: 0.6588 (OUTLIER) cc_final: 0.6128 (t) REVERT: E 331 PHE cc_start: 0.6691 (t80) cc_final: 0.6241 (m-10) REVERT: E 337 MET cc_start: 0.6102 (ppp) cc_final: 0.5832 (ppp) REVERT: E 377 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.6136 (t-170) REVERT: F 274 LYS cc_start: 0.7673 (mtpp) cc_final: 0.6943 (mtpt) REVERT: F 279 ILE cc_start: 0.7468 (mm) cc_final: 0.6541 (pt) REVERT: F 286 VAL cc_start: 0.7573 (OUTLIER) cc_final: 0.7142 (t) outliers start: 36 outliers final: 21 residues processed: 248 average time/residue: 0.2336 time to fit residues: 89.9189 Evaluate side-chains 229 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 329 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 133 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 138 optimal weight: 0.0980 chunk 168 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.204745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.164633 restraints weight = 51441.996| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 2.64 r_work: 0.4024 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16110 Z= 0.103 Angle : 0.489 4.437 21763 Z= 0.275 Chirality : 0.036 0.134 2354 Planarity : 0.004 0.039 2613 Dihedral : 7.598 57.393 2243 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.17 % Allowed : 20.07 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.19), residues: 1800 helix: -0.61 (0.14), residues: 1188 sheet: 0.13 (0.44), residues: 96 loop : -1.82 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 389 TYR 0.012 0.001 TYR E 332 PHE 0.011 0.001 PHE D 372 TRP 0.012 0.001 TRP C 143 HIS 0.009 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00220 (16092) covalent geometry : angle 0.48894 (21727) SS BOND : bond 0.00119 ( 18) SS BOND : angle 0.22243 ( 36) hydrogen bonds : bond 0.04262 ( 762) hydrogen bonds : angle 4.27258 ( 2232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.726 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8024 (tp30) cc_final: 0.7407 (tp30) REVERT: A 133 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7956 (t) REVERT: A 140 SER cc_start: 0.7916 (t) cc_final: 0.7333 (p) REVERT: A 279 ILE cc_start: 0.7278 (mm) cc_final: 0.6383 (pt) REVERT: A 284 TYR cc_start: 0.7755 (t80) cc_final: 0.7453 (t80) REVERT: A 307 THR cc_start: 0.9058 (p) cc_final: 0.8721 (t) REVERT: A 331 PHE cc_start: 0.6758 (t80) cc_final: 0.6087 (m-10) REVERT: A 358 GLU cc_start: 0.5528 (tt0) cc_final: 0.5192 (tp30) REVERT: A 377 HIS cc_start: 0.6473 (OUTLIER) cc_final: 0.5857 (t-170) REVERT: A 389 ARG cc_start: 0.6135 (ttm110) cc_final: 0.5861 (mtp-110) REVERT: B 140 SER cc_start: 0.8070 (t) cc_final: 0.7490 (p) REVERT: B 279 ILE cc_start: 0.6906 (mm) cc_final: 0.6008 (pt) REVERT: B 307 THR cc_start: 0.8971 (p) cc_final: 0.8650 (t) REVERT: B 329 VAL cc_start: 0.6427 (OUTLIER) cc_final: 0.6088 (t) REVERT: B 330 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.7031 (tt) REVERT: B 337 MET cc_start: 0.5974 (ppp) cc_final: 0.5599 (ppp) REVERT: B 375 MET cc_start: 0.7696 (mtt) cc_final: 0.7341 (mtt) REVERT: B 377 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.6028 (t-170) REVERT: C 279 ILE cc_start: 0.6867 (mm) cc_final: 0.5955 (pt) REVERT: C 286 VAL cc_start: 0.7212 (OUTLIER) cc_final: 0.6829 (t) REVERT: C 309 ARG cc_start: 0.7861 (tpt-90) cc_final: 0.7480 (mmm160) REVERT: C 330 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6664 (tp) REVERT: C 331 PHE cc_start: 0.6565 (t80) cc_final: 0.6276 (m-10) REVERT: C 377 HIS cc_start: 0.6469 (OUTLIER) cc_final: 0.5889 (t-170) REVERT: D 115 GLU cc_start: 0.7982 (tp30) cc_final: 0.7351 (tp30) REVERT: D 140 SER cc_start: 0.7745 (t) cc_final: 0.7198 (p) REVERT: D 145 LYS cc_start: 0.7396 (mmtt) cc_final: 0.6206 (ttpt) REVERT: D 255 GLU cc_start: 0.6323 (mt-10) cc_final: 0.6096 (pt0) REVERT: D 279 ILE cc_start: 0.7322 (mm) cc_final: 0.6407 (pt) REVERT: D 284 TYR cc_start: 0.7633 (t80) cc_final: 0.7252 (t80) REVERT: D 331 PHE cc_start: 0.6767 (t80) cc_final: 0.6139 (m-10) REVERT: E 133 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7804 (t) REVERT: E 140 SER cc_start: 0.8072 (t) cc_final: 0.7539 (p) REVERT: E 309 ARG cc_start: 0.7974 (tpt-90) cc_final: 0.7480 (tpp80) REVERT: E 329 VAL cc_start: 0.6340 (OUTLIER) cc_final: 0.5941 (t) REVERT: E 330 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6868 (tt) REVERT: E 331 PHE cc_start: 0.6644 (t80) cc_final: 0.6248 (m-10) REVERT: E 337 MET cc_start: 0.6003 (ppp) cc_final: 0.5616 (ppp) REVERT: E 358 GLU cc_start: 0.5534 (tt0) cc_final: 0.5077 (tp30) REVERT: E 377 HIS cc_start: 0.6690 (OUTLIER) cc_final: 0.6105 (t-170) REVERT: F 279 ILE cc_start: 0.7319 (mm) cc_final: 0.6472 (pt) REVERT: F 286 VAL cc_start: 0.7308 (OUTLIER) cc_final: 0.6941 (t) REVERT: F 331 PHE cc_start: 0.6702 (t80) cc_final: 0.6200 (m-10) outliers start: 37 outliers final: 21 residues processed: 237 average time/residue: 0.2351 time to fit residues: 86.2051 Evaluate side-chains 228 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 329 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS E 253 HIS ** F 132 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 = 0.4505 r_free = 0.4505 target = 0.200424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.157839 restraints weight = 52365.262| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.74 r_work: 0.3921 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16110 Z= 0.167 Angle : 0.535 4.321 21763 Z= 0.302 Chirality : 0.038 0.138 2354 Planarity : 0.004 0.038 2613 Dihedral : 7.986 59.124 2243 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.70 % Allowed : 18.49 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.19), residues: 1800 helix: -0.59 (0.14), residues: 1194 sheet: 0.54 (0.47), residues: 96 loop : -1.83 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 389 TYR 0.020 0.001 TYR E 332 PHE 0.015 0.002 PHE E 125 TRP 0.018 0.001 TRP A 143 HIS 0.019 0.002 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00378 (16092) covalent geometry : angle 0.53533 (21727) SS BOND : bond 0.00195 ( 18) SS BOND : angle 0.25805 ( 36) hydrogen bonds : bond 0.04616 ( 762) hydrogen bonds : angle 4.36317 ( 2232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 0.654 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8278 (tp30) cc_final: 0.7587 (tp30) REVERT: A 133 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7939 (t) REVERT: A 140 SER cc_start: 0.7974 (t) cc_final: 0.7405 (p) REVERT: A 279 ILE cc_start: 0.7512 (mm) cc_final: 0.6588 (pt) REVERT: A 284 TYR cc_start: 0.7841 (t80) cc_final: 0.7572 (t80) REVERT: A 307 THR cc_start: 0.9107 (p) cc_final: 0.8773 (t) REVERT: A 309 ARG cc_start: 0.8090 (tpt-90) cc_final: 0.7585 (tpp80) REVERT: A 331 PHE cc_start: 0.7000 (t80) cc_final: 0.6336 (m-10) REVERT: A 332 TYR cc_start: 0.7917 (t80) cc_final: 0.7700 (t80) REVERT: A 358 GLU cc_start: 0.5529 (tt0) cc_final: 0.5201 (tp30) REVERT: A 377 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.5954 (t-170) REVERT: B 110 ASP cc_start: 0.7959 (m-30) cc_final: 0.7738 (t0) REVERT: B 140 SER cc_start: 0.8044 (t) cc_final: 0.7451 (p) REVERT: B 279 ILE cc_start: 0.7216 (mm) cc_final: 0.6339 (pt) REVERT: B 307 THR cc_start: 0.9073 (p) cc_final: 0.8737 (t) REVERT: B 329 VAL cc_start: 0.6479 (OUTLIER) cc_final: 0.6164 (t) REVERT: B 331 PHE cc_start: 0.7031 (t80) cc_final: 0.6350 (m-10) REVERT: B 335 ILE cc_start: 0.4870 (OUTLIER) cc_final: 0.4602 (mt) REVERT: B 337 MET cc_start: 0.6033 (ppp) cc_final: 0.5653 (ppp) REVERT: B 348 LEU cc_start: 0.5040 (OUTLIER) cc_final: 0.4719 (pp) REVERT: B 377 HIS cc_start: 0.6626 (OUTLIER) cc_final: 0.6034 (t-170) REVERT: C 279 ILE cc_start: 0.7154 (mm) cc_final: 0.6259 (pt) REVERT: C 286 VAL cc_start: 0.7307 (OUTLIER) cc_final: 0.6940 (t) REVERT: C 309 ARG cc_start: 0.8092 (tpt-90) cc_final: 0.7583 (mmm160) REVERT: C 330 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6822 (tp) REVERT: C 331 PHE cc_start: 0.6774 (t80) cc_final: 0.6315 (m-10) REVERT: C 335 ILE cc_start: 0.4983 (OUTLIER) cc_final: 0.4571 (mt) REVERT: C 377 HIS cc_start: 0.6423 (OUTLIER) cc_final: 0.5846 (t-170) REVERT: D 115 GLU cc_start: 0.8197 (tp30) cc_final: 0.7502 (tp30) REVERT: D 133 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7927 (t) REVERT: D 140 SER cc_start: 0.7876 (t) cc_final: 0.7308 (p) REVERT: D 279 ILE cc_start: 0.7473 (mm) cc_final: 0.6566 (pt) REVERT: D 284 TYR cc_start: 0.7788 (t80) cc_final: 0.7363 (t80) REVERT: D 331 PHE cc_start: 0.6983 (t80) cc_final: 0.6416 (m-10) REVERT: E 124 TYR cc_start: 0.8853 (m-10) cc_final: 0.8634 (m-10) REVERT: E 133 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7894 (t) REVERT: E 140 SER cc_start: 0.7959 (t) cc_final: 0.7376 (p) REVERT: E 309 ARG cc_start: 0.7900 (tpt-90) cc_final: 0.7429 (tpp80) REVERT: E 329 VAL cc_start: 0.6412 (OUTLIER) cc_final: 0.6059 (t) REVERT: E 331 PHE cc_start: 0.6841 (t80) cc_final: 0.6221 (m-10) REVERT: E 335 ILE cc_start: 0.4878 (OUTLIER) cc_final: 0.4628 (mt) REVERT: E 337 MET cc_start: 0.6003 (ppp) cc_final: 0.5605 (ppp) REVERT: E 358 GLU cc_start: 0.5211 (tt0) cc_final: 0.4794 (tp30) REVERT: E 377 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.6204 (t-170) REVERT: F 279 ILE cc_start: 0.7494 (mm) cc_final: 0.7065 (tp) REVERT: F 286 VAL cc_start: 0.7413 (OUTLIER) cc_final: 0.7057 (t) REVERT: F 309 ARG cc_start: 0.8036 (tpt-90) cc_final: 0.7575 (mmm160) REVERT: F 331 PHE cc_start: 0.6849 (t80) cc_final: 0.6120 (m-10) REVERT: F 335 ILE cc_start: 0.5111 (OUTLIER) cc_final: 0.4807 (mt) outliers start: 63 outliers final: 39 residues processed: 257 average time/residue: 0.2259 time to fit residues: 90.6581 Evaluate side-chains 249 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.202988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.160376 restraints weight = 51644.590| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.75 r_work: 0.3953 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16110 Z= 0.119 Angle : 0.496 4.241 21763 Z= 0.279 Chirality : 0.037 0.124 2354 Planarity : 0.004 0.040 2613 Dihedral : 7.602 58.476 2243 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.76 % Allowed : 19.37 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1800 helix: -0.36 (0.14), residues: 1194 sheet: 0.62 (0.48), residues: 96 loop : -1.72 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 389 TYR 0.017 0.001 TYR E 332 PHE 0.011 0.001 PHE B 372 TRP 0.021 0.001 TRP A 143 HIS 0.017 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00262 (16092) covalent geometry : angle 0.49660 (21727) SS BOND : bond 0.00117 ( 18) SS BOND : angle 0.25927 ( 36) hydrogen bonds : bond 0.04210 ( 762) hydrogen bonds : angle 4.16132 ( 2232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.769 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8276 (tp30) cc_final: 0.7585 (tp30) REVERT: A 133 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7909 (t) REVERT: A 140 SER cc_start: 0.8020 (t) cc_final: 0.7432 (p) REVERT: A 279 ILE cc_start: 0.7508 (mm) cc_final: 0.6597 (pt) REVERT: A 284 TYR cc_start: 0.7860 (t80) cc_final: 0.7594 (t80) REVERT: A 307 THR cc_start: 0.9075 (p) cc_final: 0.8750 (t) REVERT: A 309 ARG cc_start: 0.8078 (tpt-90) cc_final: 0.7837 (mmm-85) REVERT: A 331 PHE cc_start: 0.6977 (t80) cc_final: 0.6279 (m-10) REVERT: A 335 ILE cc_start: 0.4858 (OUTLIER) cc_final: 0.4584 (mt) REVERT: A 358 GLU cc_start: 0.5511 (tt0) cc_final: 0.5196 (tp30) REVERT: A 377 HIS cc_start: 0.6447 (OUTLIER) cc_final: 0.5822 (t-170) REVERT: A 389 ARG cc_start: 0.6151 (ttm110) cc_final: 0.5888 (mtp-110) REVERT: B 110 ASP cc_start: 0.8059 (m-30) cc_final: 0.7688 (t0) REVERT: B 140 SER cc_start: 0.8006 (t) cc_final: 0.7412 (p) REVERT: B 307 THR cc_start: 0.9085 (p) cc_final: 0.8783 (t) REVERT: B 331 PHE cc_start: 0.7007 (t80) cc_final: 0.6430 (m-10) REVERT: B 337 MET cc_start: 0.6041 (ppp) cc_final: 0.5689 (ppp) REVERT: B 348 LEU cc_start: 0.4981 (OUTLIER) cc_final: 0.4654 (pp) REVERT: B 375 MET cc_start: 0.7445 (mtt) cc_final: 0.7102 (mtt) REVERT: B 377 HIS cc_start: 0.6593 (OUTLIER) cc_final: 0.6019 (t-170) REVERT: C 279 ILE cc_start: 0.7173 (mm) cc_final: 0.6251 (pt) REVERT: C 309 ARG cc_start: 0.8045 (tpt-90) cc_final: 0.7546 (mmm160) REVERT: C 330 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6809 (tp) REVERT: C 331 PHE cc_start: 0.6689 (t80) cc_final: 0.6361 (m-10) REVERT: C 343 MET cc_start: 0.6994 (ttm) cc_final: 0.6781 (ttm) REVERT: C 375 MET cc_start: 0.6942 (mtm) cc_final: 0.6725 (mtm) REVERT: C 377 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.5798 (t-170) REVERT: D 115 GLU cc_start: 0.8182 (tp30) cc_final: 0.7560 (tp30) REVERT: D 133 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7922 (t) REVERT: D 140 SER cc_start: 0.7868 (t) cc_final: 0.7300 (p) REVERT: D 279 ILE cc_start: 0.7462 (mm) cc_final: 0.6550 (pt) REVERT: D 331 PHE cc_start: 0.6974 (t80) cc_final: 0.6448 (m-10) REVERT: E 124 TYR cc_start: 0.8846 (m-10) cc_final: 0.8635 (m-10) REVERT: E 133 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7887 (t) REVERT: E 140 SER cc_start: 0.7927 (t) cc_final: 0.7347 (p) REVERT: E 309 ARG cc_start: 0.7861 (tpt-90) cc_final: 0.7394 (tpp80) REVERT: E 337 MET cc_start: 0.6002 (ppp) cc_final: 0.5624 (ppp) REVERT: E 358 GLU cc_start: 0.5352 (tt0) cc_final: 0.4910 (tp30) REVERT: E 377 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.6103 (t-170) REVERT: F 279 ILE cc_start: 0.7458 (mm) cc_final: 0.7083 (tp) REVERT: F 309 ARG cc_start: 0.8080 (tpt-90) cc_final: 0.7643 (mmm160) REVERT: F 331 PHE cc_start: 0.6771 (t80) cc_final: 0.6231 (m-10) outliers start: 47 outliers final: 27 residues processed: 237 average time/residue: 0.2426 time to fit residues: 88.7216 Evaluate side-chains 232 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 125 optimal weight: 0.2980 chunk 175 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.203252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.160607 restraints weight = 51682.810| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.74 r_work: 0.3950 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16110 Z= 0.119 Angle : 0.493 4.057 21763 Z= 0.277 Chirality : 0.037 0.135 2354 Planarity : 0.003 0.036 2613 Dihedral : 7.334 58.509 2238 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.29 % Allowed : 18.72 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1800 helix: -0.12 (0.15), residues: 1188 sheet: 0.79 (0.50), residues: 96 loop : -1.72 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 389 TYR 0.013 0.001 TYR C 332 PHE 0.011 0.001 PHE A 372 TRP 0.025 0.001 TRP A 143 HIS 0.006 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00265 (16092) covalent geometry : angle 0.49294 (21727) SS BOND : bond 0.00115 ( 18) SS BOND : angle 0.26446 ( 36) hydrogen bonds : bond 0.04046 ( 762) hydrogen bonds : angle 4.04049 ( 2232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 0.830 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8261 (tp30) cc_final: 0.7616 (tp30) REVERT: A 133 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7920 (t) REVERT: A 140 SER cc_start: 0.7985 (t) cc_final: 0.7385 (p) REVERT: A 284 TYR cc_start: 0.7987 (t80) cc_final: 0.7600 (t80) REVERT: A 307 THR cc_start: 0.9096 (p) cc_final: 0.8783 (t) REVERT: A 309 ARG cc_start: 0.8045 (tpt-90) cc_final: 0.7577 (tpp80) REVERT: A 331 PHE cc_start: 0.7049 (t80) cc_final: 0.6399 (m-10) REVERT: A 335 ILE cc_start: 0.4883 (OUTLIER) cc_final: 0.4630 (mt) REVERT: A 358 GLU cc_start: 0.5507 (tt0) cc_final: 0.5207 (tp30) REVERT: A 377 HIS cc_start: 0.6487 (OUTLIER) cc_final: 0.5836 (t-170) REVERT: B 140 SER cc_start: 0.8014 (t) cc_final: 0.7432 (p) REVERT: B 279 ILE cc_start: 0.7163 (mm) cc_final: 0.6834 (tp) REVERT: B 307 THR cc_start: 0.9082 (p) cc_final: 0.8801 (t) REVERT: B 331 PHE cc_start: 0.6984 (t80) cc_final: 0.6493 (m-10) REVERT: B 337 MET cc_start: 0.6061 (ppp) cc_final: 0.5719 (ppp) REVERT: B 375 MET cc_start: 0.7589 (mtt) cc_final: 0.7362 (mtt) REVERT: B 377 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6019 (t-170) REVERT: C 279 ILE cc_start: 0.7264 (mm) cc_final: 0.6200 (pt) REVERT: C 286 VAL cc_start: 0.7346 (OUTLIER) cc_final: 0.6951 (t) REVERT: C 309 ARG cc_start: 0.8075 (tpt-90) cc_final: 0.7553 (mmm160) REVERT: C 331 PHE cc_start: 0.6582 (t80) cc_final: 0.6198 (m-10) REVERT: C 343 MET cc_start: 0.6997 (ttm) cc_final: 0.6768 (ttm) REVERT: C 377 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.5904 (t-170) REVERT: D 115 GLU cc_start: 0.8197 (tp30) cc_final: 0.7586 (tp30) REVERT: D 140 SER cc_start: 0.7853 (t) cc_final: 0.7292 (p) REVERT: D 265 MET cc_start: 0.6357 (tpt) cc_final: 0.6057 (tpt) REVERT: D 279 ILE cc_start: 0.7474 (mm) cc_final: 0.6557 (pt) REVERT: D 284 TYR cc_start: 0.7727 (t80) cc_final: 0.7368 (t80) REVERT: D 286 VAL cc_start: 0.7322 (OUTLIER) cc_final: 0.7017 (t) REVERT: D 331 PHE cc_start: 0.7095 (t80) cc_final: 0.6488 (m-10) REVERT: D 335 ILE cc_start: 0.4921 (OUTLIER) cc_final: 0.4645 (mt) REVERT: E 133 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7839 (t) REVERT: E 140 SER cc_start: 0.7910 (t) cc_final: 0.7329 (p) REVERT: E 284 TYR cc_start: 0.7815 (t80) cc_final: 0.7429 (t80) REVERT: E 309 ARG cc_start: 0.7916 (tpt-90) cc_final: 0.7424 (tpp80) REVERT: E 331 PHE cc_start: 0.6968 (t80) cc_final: 0.6436 (m-10) REVERT: E 337 MET cc_start: 0.5997 (ppp) cc_final: 0.5622 (ppp) REVERT: E 358 GLU cc_start: 0.5404 (tt0) cc_final: 0.5000 (tp30) REVERT: E 377 HIS cc_start: 0.6588 (OUTLIER) cc_final: 0.6017 (t-170) REVERT: F 279 ILE cc_start: 0.7512 (mm) cc_final: 0.7196 (tp) REVERT: F 309 ARG cc_start: 0.8135 (tpt-90) cc_final: 0.7926 (mmm-85) REVERT: F 331 PHE cc_start: 0.6839 (t80) cc_final: 0.6278 (m-10) outliers start: 56 outliers final: 34 residues processed: 249 average time/residue: 0.2358 time to fit residues: 90.5880 Evaluate side-chains 242 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 340 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.201384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.158537 restraints weight = 52205.414| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.73 r_work: 0.3938 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16110 Z= 0.142 Angle : 0.517 5.170 21763 Z= 0.290 Chirality : 0.038 0.151 2354 Planarity : 0.004 0.040 2613 Dihedral : 7.568 59.639 2237 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.64 % Allowed : 18.54 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1800 helix: -0.11 (0.15), residues: 1188 sheet: 0.99 (0.52), residues: 96 loop : -1.80 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 389 TYR 0.021 0.001 TYR D 332 PHE 0.014 0.001 PHE A 372 TRP 0.025 0.001 TRP A 143 HIS 0.009 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00321 (16092) covalent geometry : angle 0.51704 (21727) SS BOND : bond 0.00163 ( 18) SS BOND : angle 0.27477 ( 36) hydrogen bonds : bond 0.04184 ( 762) hydrogen bonds : angle 4.11491 ( 2232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.722 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: 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 115 GLU cc_start: 0.8248 (tp30) cc_final: 0.7600 (tp30) REVERT: A 133 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7945 (t) REVERT: A 140 SER cc_start: 0.8002 (t) cc_final: 0.7423 (p) REVERT: A 279 ILE cc_start: 0.7356 (mm) cc_final: 0.7142 (tp) REVERT: A 284 TYR cc_start: 0.8058 (t80) cc_final: 0.7732 (t80) REVERT: A 307 THR cc_start: 0.9111 (p) cc_final: 0.8800 (t) REVERT: A 309 ARG cc_start: 0.8067 (tpt-90) cc_final: 0.7589 (tpp80) REVERT: A 331 PHE cc_start: 0.7177 (t80) cc_final: 0.6557 (m-10) REVERT: A 332 TYR cc_start: 0.7983 (t80) cc_final: 0.7752 (t80) REVERT: A 335 ILE cc_start: 0.5001 (OUTLIER) cc_final: 0.4760 (mt) REVERT: A 358 GLU cc_start: 0.5471 (tt0) cc_final: 0.5199 (tp30) REVERT: A 377 HIS cc_start: 0.6525 (OUTLIER) cc_final: 0.5868 (t-170) REVERT: B 140 SER cc_start: 0.8077 (t) cc_final: 0.7513 (p) REVERT: B 265 MET cc_start: 0.6510 (tpt) cc_final: 0.6223 (tpt) REVERT: B 279 ILE cc_start: 0.7322 (mm) cc_final: 0.7055 (tp) REVERT: B 307 THR cc_start: 0.9164 (p) cc_final: 0.8882 (t) REVERT: B 309 ARG cc_start: 0.7952 (tpt-90) cc_final: 0.7478 (tpp80) REVERT: B 331 PHE cc_start: 0.7097 (t80) cc_final: 0.6558 (m-10) REVERT: B 335 ILE cc_start: 0.4849 (OUTLIER) cc_final: 0.4609 (mt) REVERT: B 337 MET cc_start: 0.6105 (ppp) cc_final: 0.5758 (ppp) REVERT: B 351 TYR cc_start: 0.6568 (t80) cc_final: 0.6279 (t80) REVERT: B 377 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6019 (t-170) REVERT: C 279 ILE cc_start: 0.7338 (mm) cc_final: 0.6973 (tp) REVERT: C 286 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7117 (t) REVERT: C 309 ARG cc_start: 0.8093 (tpt-90) cc_final: 0.7568 (mmm160) REVERT: C 331 PHE cc_start: 0.6779 (t80) cc_final: 0.6235 (m-10) REVERT: C 335 ILE cc_start: 0.5031 (OUTLIER) cc_final: 0.4727 (mt) REVERT: C 343 MET cc_start: 0.6987 (ttm) cc_final: 0.6782 (ttm) REVERT: C 377 HIS cc_start: 0.6493 (OUTLIER) cc_final: 0.5865 (t-170) REVERT: D 27 PHE cc_start: 0.5779 (m-80) cc_final: 0.5556 (m-10) REVERT: D 115 GLU cc_start: 0.8234 (tp30) cc_final: 0.7607 (tp30) REVERT: D 133 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7968 (t) REVERT: D 140 SER cc_start: 0.7878 (t) cc_final: 0.7327 (p) REVERT: D 265 MET cc_start: 0.6425 (tpt) cc_final: 0.6151 (tpt) REVERT: D 279 ILE cc_start: 0.7545 (mm) cc_final: 0.7293 (tp) REVERT: D 284 TYR cc_start: 0.7768 (t80) cc_final: 0.7442 (t80) REVERT: D 286 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.7158 (t) REVERT: D 331 PHE cc_start: 0.7306 (t80) cc_final: 0.6660 (m-10) REVERT: D 335 ILE cc_start: 0.4946 (OUTLIER) cc_final: 0.4695 (mt) REVERT: E 140 SER cc_start: 0.8097 (t) cc_final: 0.7519 (p) REVERT: E 265 MET cc_start: 0.6514 (tpt) cc_final: 0.6226 (tpt) REVERT: E 284 TYR cc_start: 0.7938 (t80) cc_final: 0.7465 (t80) REVERT: E 309 ARG cc_start: 0.7943 (tpt-90) cc_final: 0.7450 (tpp80) REVERT: E 331 PHE cc_start: 0.7069 (t80) cc_final: 0.6451 (m-10) REVERT: E 335 ILE cc_start: 0.4787 (OUTLIER) cc_final: 0.4542 (mt) REVERT: E 337 MET cc_start: 0.6015 (ppp) cc_final: 0.5628 (ppp) REVERT: E 358 GLU cc_start: 0.5320 (tt0) cc_final: 0.4906 (tp30) REVERT: E 377 HIS cc_start: 0.6628 (OUTLIER) cc_final: 0.6070 (t-170) REVERT: F 279 ILE cc_start: 0.7627 (mm) cc_final: 0.7382 (tp) REVERT: F 309 ARG cc_start: 0.8143 (tpt-90) cc_final: 0.7678 (mmm160) REVERT: F 331 PHE cc_start: 0.7045 (t80) cc_final: 0.6345 (m-10) REVERT: F 335 ILE cc_start: 0.5083 (OUTLIER) cc_final: 0.4818 (mt) outliers start: 62 outliers final: 37 residues processed: 259 average time/residue: 0.2397 time to fit residues: 95.1839 Evaluate side-chains 259 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 104 optimal weight: 3.9990 chunk 168 optimal weight: 0.0970 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 23 optimal weight: 0.0010 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** F 132 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 = 0.4442 r_free = 0.4442 target = 0.202617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158320 restraints weight = 52169.907| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.88 r_work: 0.3879 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16110 Z= 0.118 Angle : 0.499 6.536 21763 Z= 0.279 Chirality : 0.038 0.191 2354 Planarity : 0.003 0.036 2613 Dihedral : 7.338 59.035 2237 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.93 % Allowed : 19.13 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1800 helix: 0.06 (0.15), residues: 1194 sheet: 0.85 (0.51), residues: 96 loop : -1.75 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 389 TYR 0.014 0.001 TYR F 332 PHE 0.014 0.001 PHE A 372 TRP 0.023 0.001 TRP A 143 HIS 0.011 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00264 (16092) covalent geometry : angle 0.49920 (21727) SS BOND : bond 0.00111 ( 18) SS BOND : angle 0.28770 ( 36) hydrogen bonds : bond 0.03948 ( 762) hydrogen bonds : angle 3.99533 ( 2232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.679 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8389 (tp30) cc_final: 0.7718 (tp30) REVERT: A 133 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7920 (t) REVERT: A 140 SER cc_start: 0.7892 (t) cc_final: 0.7339 (p) REVERT: A 279 ILE cc_start: 0.7340 (mm) cc_final: 0.7096 (tp) REVERT: A 284 TYR cc_start: 0.8094 (t80) cc_final: 0.7674 (t80) REVERT: A 307 THR cc_start: 0.9125 (p) cc_final: 0.8774 (t) REVERT: A 309 ARG cc_start: 0.7930 (tpt-90) cc_final: 0.7493 (tpp80) REVERT: A 331 PHE cc_start: 0.7069 (t80) cc_final: 0.6456 (m-10) REVERT: A 332 TYR cc_start: 0.7932 (t80) cc_final: 0.7633 (t80) REVERT: A 358 GLU cc_start: 0.5334 (tt0) cc_final: 0.5063 (tp30) REVERT: A 377 HIS cc_start: 0.6050 (OUTLIER) cc_final: 0.5517 (t-170) REVERT: B 140 SER cc_start: 0.7922 (t) cc_final: 0.7366 (p) REVERT: B 265 MET cc_start: 0.6310 (tpt) cc_final: 0.6013 (tpt) REVERT: B 279 ILE cc_start: 0.7214 (mm) cc_final: 0.6976 (tp) REVERT: B 307 THR cc_start: 0.9172 (p) cc_final: 0.8857 (t) REVERT: B 309 ARG cc_start: 0.7790 (tpt-90) cc_final: 0.7331 (tpp80) REVERT: B 331 PHE cc_start: 0.7042 (t80) cc_final: 0.6509 (m-10) REVERT: B 337 MET cc_start: 0.6002 (ppp) cc_final: 0.5667 (ppp) REVERT: B 351 TYR cc_start: 0.6315 (t80) cc_final: 0.6020 (t80) REVERT: B 377 HIS cc_start: 0.6384 (OUTLIER) cc_final: 0.5860 (t-170) REVERT: C 279 ILE cc_start: 0.7351 (mm) cc_final: 0.7028 (tp) REVERT: C 286 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.6906 (t) REVERT: C 309 ARG cc_start: 0.7953 (tpt-90) cc_final: 0.7363 (mmm160) REVERT: C 331 PHE cc_start: 0.6876 (t80) cc_final: 0.6248 (m-10) REVERT: C 340 LEU cc_start: 0.4234 (OUTLIER) cc_final: 0.3949 (tp) REVERT: C 343 MET cc_start: 0.6913 (ttm) cc_final: 0.6700 (ttm) REVERT: C 377 HIS cc_start: 0.6206 (OUTLIER) cc_final: 0.5675 (t-170) REVERT: C 389 ARG cc_start: 0.5851 (ttm110) cc_final: 0.5441 (ttm170) REVERT: D 115 GLU cc_start: 0.8326 (tp30) cc_final: 0.7693 (tp30) REVERT: D 133 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7943 (t) REVERT: D 140 SER cc_start: 0.7784 (t) cc_final: 0.7236 (p) REVERT: D 265 MET cc_start: 0.6191 (tpt) cc_final: 0.5903 (tpt) REVERT: D 279 ILE cc_start: 0.7487 (mm) cc_final: 0.7267 (tp) REVERT: D 284 TYR cc_start: 0.7729 (t80) cc_final: 0.7375 (t80) REVERT: D 331 PHE cc_start: 0.7225 (t80) cc_final: 0.6621 (m-10) REVERT: D 332 TYR cc_start: 0.7852 (t80) cc_final: 0.7423 (t80) REVERT: E 140 SER cc_start: 0.7912 (t) cc_final: 0.7328 (p) REVERT: E 284 TYR cc_start: 0.7943 (t80) cc_final: 0.7409 (t80) REVERT: E 309 ARG cc_start: 0.7787 (tpt-90) cc_final: 0.7314 (tpp80) REVERT: E 331 PHE cc_start: 0.6993 (t80) cc_final: 0.6335 (m-10) REVERT: E 335 ILE cc_start: 0.4411 (OUTLIER) cc_final: 0.4179 (mt) REVERT: E 337 MET cc_start: 0.5894 (ppp) cc_final: 0.5509 (ppp) REVERT: E 358 GLU cc_start: 0.5108 (tt0) cc_final: 0.4717 (tp30) REVERT: E 377 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.5875 (t-170) REVERT: E 399 GLU cc_start: 0.7268 (tt0) cc_final: 0.6980 (tt0) REVERT: F 265 MET cc_start: 0.6239 (tpt) cc_final: 0.5953 (tpt) REVERT: F 279 ILE cc_start: 0.7632 (mm) cc_final: 0.7421 (tp) REVERT: F 309 ARG cc_start: 0.8010 (tpt-90) cc_final: 0.7793 (mmm-85) REVERT: F 331 PHE cc_start: 0.7010 (t80) cc_final: 0.6290 (m-10) outliers start: 50 outliers final: 36 residues processed: 250 average time/residue: 0.2395 time to fit residues: 91.2105 Evaluate side-chains 254 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 143 TRP Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** F 132 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 = 0.4434 r_free = 0.4434 target = 0.201676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157375 restraints weight = 52240.276| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.87 r_work: 0.3865 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16110 Z= 0.134 Angle : 0.520 7.429 21763 Z= 0.289 Chirality : 0.038 0.205 2354 Planarity : 0.004 0.039 2613 Dihedral : 7.421 59.960 2236 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.05 % Allowed : 19.19 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1800 helix: -0.01 (0.15), residues: 1188 sheet: 0.90 (0.51), residues: 96 loop : -1.81 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 389 TYR 0.015 0.001 TYR D 332 PHE 0.011 0.001 PHE A 372 TRP 0.022 0.001 TRP A 143 HIS 0.014 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00303 (16092) covalent geometry : angle 0.52021 (21727) SS BOND : bond 0.00131 ( 18) SS BOND : angle 0.29266 ( 36) hydrogen bonds : bond 0.03993 ( 762) hydrogen bonds : angle 4.05202 ( 2232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 0.603 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8383 (tp30) cc_final: 0.7702 (tp30) REVERT: A 133 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7937 (t) REVERT: A 140 SER cc_start: 0.7916 (t) cc_final: 0.7362 (p) REVERT: A 279 ILE cc_start: 0.7452 (mm) cc_final: 0.7225 (tp) REVERT: A 284 TYR cc_start: 0.8077 (t80) cc_final: 0.7643 (t80) REVERT: A 307 THR cc_start: 0.9127 (p) cc_final: 0.8775 (t) REVERT: A 309 ARG cc_start: 0.7943 (tpt-90) cc_final: 0.7499 (tpp80) REVERT: A 331 PHE cc_start: 0.7137 (t80) cc_final: 0.6456 (m-10) REVERT: A 332 TYR cc_start: 0.7983 (t80) cc_final: 0.7692 (t80) REVERT: A 335 ILE cc_start: 0.4720 (OUTLIER) cc_final: 0.4502 (mt) REVERT: A 358 GLU cc_start: 0.5219 (tt0) cc_final: 0.4937 (tp30) REVERT: A 377 HIS cc_start: 0.6068 (OUTLIER) cc_final: 0.5526 (t-170) REVERT: B 140 SER cc_start: 0.7922 (t) cc_final: 0.7368 (p) REVERT: B 265 MET cc_start: 0.6370 (tpt) cc_final: 0.6065 (tpt) REVERT: B 274 LYS cc_start: 0.7203 (ttmm) cc_final: 0.6863 (ttpt) REVERT: B 279 ILE cc_start: 0.7254 (mm) cc_final: 0.7038 (tp) REVERT: B 307 THR cc_start: 0.9181 (p) cc_final: 0.8868 (t) REVERT: B 309 ARG cc_start: 0.7798 (tpt-90) cc_final: 0.7338 (tpp80) REVERT: B 331 PHE cc_start: 0.7075 (t80) cc_final: 0.6530 (m-10) REVERT: B 337 MET cc_start: 0.5961 (ppp) cc_final: 0.5627 (ppp) REVERT: B 351 TYR cc_start: 0.6326 (t80) cc_final: 0.6031 (t80) REVERT: B 377 HIS cc_start: 0.6412 (OUTLIER) cc_final: 0.5881 (t-170) REVERT: C 279 ILE cc_start: 0.7409 (mm) cc_final: 0.7114 (tp) REVERT: C 286 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.6925 (t) REVERT: C 309 ARG cc_start: 0.7975 (tpt-90) cc_final: 0.7721 (mmm-85) REVERT: C 331 PHE cc_start: 0.6878 (t80) cc_final: 0.6231 (m-10) REVERT: C 340 LEU cc_start: 0.4252 (OUTLIER) cc_final: 0.3958 (tp) REVERT: C 343 MET cc_start: 0.6937 (ttm) cc_final: 0.6711 (ttm) REVERT: C 377 HIS cc_start: 0.6231 (OUTLIER) cc_final: 0.5680 (t-170) REVERT: D 115 GLU cc_start: 0.8347 (tp30) cc_final: 0.7693 (tp30) REVERT: D 133 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7943 (t) REVERT: D 140 SER cc_start: 0.7868 (t) cc_final: 0.7329 (p) REVERT: D 265 MET cc_start: 0.6254 (tpt) cc_final: 0.5960 (tpt) REVERT: D 279 ILE cc_start: 0.7412 (mm) cc_final: 0.7197 (tp) REVERT: D 284 TYR cc_start: 0.7814 (t80) cc_final: 0.7440 (t80) REVERT: D 331 PHE cc_start: 0.7335 (t80) cc_final: 0.6617 (m-10) REVERT: D 335 ILE cc_start: 0.4660 (OUTLIER) cc_final: 0.4425 (mt) REVERT: D 389 ARG cc_start: 0.6049 (ttm110) cc_final: 0.5756 (mtp-110) REVERT: E 115 GLU cc_start: 0.8218 (tp30) cc_final: 0.7951 (tp30) REVERT: E 124 TYR cc_start: 0.8877 (m-10) cc_final: 0.8676 (m-10) REVERT: E 140 SER cc_start: 0.7858 (t) cc_final: 0.7288 (p) REVERT: E 284 TYR cc_start: 0.7974 (t80) cc_final: 0.7427 (t80) REVERT: E 309 ARG cc_start: 0.7806 (tpt-90) cc_final: 0.7329 (tpp80) REVERT: E 331 PHE cc_start: 0.7089 (t80) cc_final: 0.6431 (m-10) REVERT: E 335 ILE cc_start: 0.4539 (OUTLIER) cc_final: 0.4296 (mt) REVERT: E 337 MET cc_start: 0.5907 (ppp) cc_final: 0.5531 (ppp) REVERT: E 358 GLU cc_start: 0.5167 (tt0) cc_final: 0.4759 (tp30) REVERT: E 377 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.5921 (t-170) REVERT: E 389 ARG cc_start: 0.5647 (ttm110) cc_final: 0.5430 (mtp-110) REVERT: F 279 ILE cc_start: 0.7674 (mm) cc_final: 0.7461 (tp) REVERT: F 286 VAL cc_start: 0.7310 (OUTLIER) cc_final: 0.7004 (t) REVERT: F 309 ARG cc_start: 0.8031 (tpt-90) cc_final: 0.7809 (mmm-85) REVERT: F 331 PHE cc_start: 0.7086 (t80) cc_final: 0.6369 (m-10) outliers start: 52 outliers final: 40 residues processed: 250 average time/residue: 0.2441 time to fit residues: 92.6926 Evaluate side-chains 258 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 143 TRP Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 9 optimal weight: 0.0370 chunk 64 optimal weight: 0.0770 chunk 118 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.204045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159732 restraints weight = 52239.224| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.90 r_work: 0.3890 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16110 Z= 0.103 Angle : 0.501 7.834 21763 Z= 0.277 Chirality : 0.038 0.228 2354 Planarity : 0.004 0.036 2613 Dihedral : 7.154 59.780 2236 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.52 % Allowed : 19.84 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1800 helix: 0.11 (0.15), residues: 1188 sheet: 0.74 (0.50), residues: 96 loop : -1.74 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 389 TYR 0.013 0.001 TYR F 332 PHE 0.011 0.001 PHE D 372 TRP 0.022 0.001 TRP A 143 HIS 0.008 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00225 (16092) covalent geometry : angle 0.50114 (21727) SS BOND : bond 0.00102 ( 18) SS BOND : angle 0.32933 ( 36) hydrogen bonds : bond 0.03769 ( 762) hydrogen bonds : angle 3.94225 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6530.04 seconds wall clock time: 111 minutes 33.78 seconds (6693.78 seconds total)