Starting phenix.real_space_refine on Sat Jun 6 00:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l2o_62778/06_2026/9l2o_62778_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l2o_62778/06_2026/9l2o_62778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l2o_62778/06_2026/9l2o_62778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l2o_62778/06_2026/9l2o_62778.map" model { file = "/net/cci-nas-00/data/ceres_data/9l2o_62778/06_2026/9l2o_62778_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l2o_62778/06_2026/9l2o_62778_neut.cif" } resolution = 2.86 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= 0.004 sd= 0.047 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 Zn 16 6.06 5 S 80 5.16 5 Cl 8 4.86 5 C 15176 2.51 5 N 4320 2.21 5 O 4624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24224 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2998 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2998 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2998 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2998 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2998 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2998 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2998 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2998 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.65, per 1000 atoms: 0.23 Number of scatterers: 24224 At special positions: 0 Unit cell: (139.5, 140.43, 105.09, 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) Zn 16 29.99 Cl 8 17.00 S 80 16.00 O 4624 8.00 N 4320 7.00 C 15176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " 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 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 271 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 251 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 42.9% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.745A pdb=" N PHE B 99 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.682A pdb=" N TYR B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 293 through 305 removed outlier: 3.695A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 354 through 363 removed outlier: 4.121A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.663A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 removed outlier: 3.522A pdb=" N LEU B 413 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.745A pdb=" N PHE A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.683A pdb=" N TYR A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY A 112 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.696A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 354 through 363 removed outlier: 4.122A pdb=" N ILE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.664A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 removed outlier: 3.521A pdb=" N LEU A 413 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.745A pdb=" N PHE C 99 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.683A pdb=" N TYR C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY C 112 " --> pdb=" O TYR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 171 through 179 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 190 through 204 Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.695A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 322 Processing helix chain 'C' and resid 325 through 336 Processing helix chain 'C' and resid 354 through 363 removed outlier: 4.122A pdb=" N ILE C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 373 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.664A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 removed outlier: 3.523A pdb=" N LEU C 413 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.745A pdb=" N PHE D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.683A pdb=" N TYR D 108 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 171 through 179 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 293 through 305 removed outlier: 3.696A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 354 through 363 removed outlier: 4.121A pdb=" N ILE D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.663A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 414 removed outlier: 3.521A pdb=" N LEU D 413 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.745A pdb=" N PHE E 99 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.682A pdb=" N TYR E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY E 112 " --> pdb=" O TYR E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 276 through 287 Processing helix chain 'E' and resid 293 through 305 removed outlier: 3.695A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS E 305 " --> pdb=" O ALA E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 Processing helix chain 'E' and resid 325 through 336 Processing helix chain 'E' and resid 354 through 363 removed outlier: 4.121A pdb=" N ILE E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 375 through 383 removed outlier: 3.663A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 414 removed outlier: 3.522A pdb=" N LEU E 413 " --> pdb=" O ASN E 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 100 removed outlier: 3.745A pdb=" N PHE F 99 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 removed outlier: 3.682A pdb=" N TYR F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY F 112 " --> pdb=" O TYR F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 Processing helix chain 'F' and resid 171 through 179 Processing helix chain 'F' and resid 182 through 186 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 276 through 287 Processing helix chain 'F' and resid 293 through 305 removed outlier: 3.695A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS F 305 " --> pdb=" O ALA F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 Processing helix chain 'F' and resid 325 through 336 Processing helix chain 'F' and resid 354 through 363 removed outlier: 4.121A pdb=" N ILE F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 373 Processing helix chain 'F' and resid 375 through 383 removed outlier: 3.664A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 414 removed outlier: 3.521A pdb=" N LEU F 413 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 100 removed outlier: 3.745A pdb=" N PHE G 99 " --> pdb=" O SER G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 120 removed outlier: 3.682A pdb=" N TYR G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG G 109 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY G 112 " --> pdb=" O TYR G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 171 through 179 Processing helix chain 'G' and resid 182 through 186 Processing helix chain 'G' and resid 190 through 204 Processing helix chain 'G' and resid 230 through 244 Processing helix chain 'G' and resid 254 through 265 Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 293 through 305 removed outlier: 3.695A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS G 305 " --> pdb=" O ALA G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 322 Processing helix chain 'G' and resid 325 through 336 Processing helix chain 'G' and resid 354 through 363 removed outlier: 4.122A pdb=" N ILE G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 375 through 383 removed outlier: 3.664A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 414 removed outlier: 3.523A pdb=" N LEU G 413 " --> pdb=" O ASN G 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.745A pdb=" N PHE H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.684A pdb=" N TYR H 108 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG H 109 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY H 112 " --> pdb=" O TYR H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 Processing helix chain 'H' and resid 171 through 179 Processing helix chain 'H' and resid 182 through 186 Processing helix chain 'H' and resid 190 through 204 Processing helix chain 'H' and resid 230 through 244 Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 276 through 287 Processing helix chain 'H' and resid 293 through 305 removed outlier: 3.696A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS H 305 " --> pdb=" O ALA H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 322 Processing helix chain 'H' and resid 325 through 336 Processing helix chain 'H' and resid 354 through 363 removed outlier: 4.122A pdb=" N ILE H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 373 Processing helix chain 'H' and resid 375 through 383 removed outlier: 3.663A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 414 removed outlier: 3.521A pdb=" N LEU H 413 " --> pdb=" O ASN H 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 39 removed outlier: 6.312A pdb=" N THR B 43 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 54 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 45 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 39 removed outlier: 13.821A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 13.287A pdb=" N ARG B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.137A pdb=" N LEU B 25 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ARG B 73 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS B 27 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N PHE B 31 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 418 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.319A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP B 81 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR B 123 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N PHE B 151 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 125 " --> pdb=" O PHE B 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.502A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 268 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 37 through 39 removed outlier: 6.312A pdb=" N THR A 43 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 54 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 45 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 37 through 39 removed outlier: 13.821A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 13.287A pdb=" N ARG A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.137A pdb=" N LEU A 25 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N ARG A 73 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS A 27 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N PHE A 31 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A 418 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.319A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP A 81 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A 123 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N PHE A 151 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 125 " --> pdb=" O PHE A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.502A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 268 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 39 removed outlier: 6.312A pdb=" N THR C 43 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU C 54 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C 45 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39 removed outlier: 13.821A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 13.287A pdb=" N ARG C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.137A pdb=" N LEU C 25 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ARG C 73 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYS C 27 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N PHE C 31 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 418 " --> pdb=" O PHE C 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 84 removed outlier: 6.318A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR C 123 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N PHE C 151 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 125 " --> pdb=" O PHE C 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.502A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 268 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 39 removed outlier: 6.312A pdb=" N THR D 43 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU D 54 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 45 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 37 through 39 removed outlier: 13.821A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.286A pdb=" N ARG D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.136A pdb=" N LEU D 25 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ARG D 73 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS D 27 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N PHE D 31 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL D 418 " --> pdb=" O PHE D 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.319A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR D 123 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N PHE D 151 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL D 125 " --> pdb=" O PHE D 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.501A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 268 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 39 removed outlier: 6.312A pdb=" N THR E 43 " --> pdb=" O LEU E 54 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU E 54 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL E 45 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 37 through 39 removed outlier: 13.821A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 13.287A pdb=" N ARG E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.136A pdb=" N LEU E 25 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ARG E 73 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS E 27 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL E 418 " --> pdb=" O PHE E 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.318A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR E 123 " --> pdb=" O ARG E 149 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N PHE E 151 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL E 125 " --> pdb=" O PHE E 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 209 through 212 removed outlier: 6.502A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER E 268 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 39 removed outlier: 6.312A pdb=" N THR F 43 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU F 54 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL F 45 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 39 removed outlier: 13.821A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 13.286A pdb=" N ARG F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.136A pdb=" N LEU F 25 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ARG F 73 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS F 27 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL F 418 " --> pdb=" O PHE F 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.319A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR F 123 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N PHE F 151 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL F 125 " --> pdb=" O PHE F 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.502A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER F 268 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 37 through 39 removed outlier: 6.313A pdb=" N THR G 43 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL G 45 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 37 through 39 removed outlier: 13.821A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 13.288A pdb=" N ARG G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.137A pdb=" N LEU G 25 " --> pdb=" O ARG G 71 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ARG G 73 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS G 27 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N PHE G 31 " --> pdb=" O PRO G 77 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL G 418 " --> pdb=" O PHE G 425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.318A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR G 123 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N PHE G 151 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL G 125 " --> pdb=" O PHE G 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 209 through 212 removed outlier: 6.503A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER G 268 " --> pdb=" O VAL G 248 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 39 removed outlier: 6.312A pdb=" N THR H 43 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL H 45 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 37 through 39 removed outlier: 13.821A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 13.286A pdb=" N ARG H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.136A pdb=" N LEU H 25 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N ARG H 73 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS H 27 " --> pdb=" O ARG H 73 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL H 418 " --> pdb=" O PHE H 425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.319A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR H 123 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N PHE H 151 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL H 125 " --> pdb=" O PHE H 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'H' and resid 209 through 212 removed outlier: 6.501A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER H 268 " --> pdb=" O VAL H 248 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5557 1.33 - 1.45: 5311 1.45 - 1.57: 13684 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 24704 Sorted by residual: bond pdb=" CAD 97U H 503 " pdb=" CAG 97U H 503 " ideal model delta sigma weight residual 1.495 1.374 0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" CAD 97U F 503 " pdb=" CAG 97U F 503 " ideal model delta sigma weight residual 1.495 1.374 0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" CAD 97U E 503 " pdb=" CAG 97U E 503 " ideal model delta sigma weight residual 1.495 1.374 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CB 97U H 503 " pdb=" CG 97U H 503 " ideal model delta sigma weight residual 1.505 1.384 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CAD 97U B 503 " pdb=" CAG 97U B 503 " ideal model delta sigma weight residual 1.495 1.374 0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 24699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 32539 1.47 - 2.94: 710 2.94 - 4.42: 215 4.42 - 5.89: 48 5.89 - 7.36: 16 Bond angle restraints: 33528 Sorted by residual: angle pdb=" C GLU D 270 " pdb=" N HIS D 271 " pdb=" CA HIS D 271 " ideal model delta sigma weight residual 122.87 117.93 4.94 1.44e+00 4.82e-01 1.18e+01 angle pdb=" C GLU G 270 " pdb=" N HIS G 271 " pdb=" CA HIS G 271 " ideal model delta sigma weight residual 122.87 117.96 4.91 1.44e+00 4.82e-01 1.16e+01 angle pdb=" C GLU C 270 " pdb=" N HIS C 271 " pdb=" CA HIS C 271 " ideal model delta sigma weight residual 122.87 117.97 4.90 1.44e+00 4.82e-01 1.16e+01 angle pdb=" C GLU H 270 " pdb=" N HIS H 271 " pdb=" CA HIS H 271 " ideal model delta sigma weight residual 122.87 117.97 4.90 1.44e+00 4.82e-01 1.16e+01 angle pdb=" C GLU A 270 " pdb=" N HIS A 271 " pdb=" CA HIS A 271 " ideal model delta sigma weight residual 122.87 117.98 4.89 1.44e+00 4.82e-01 1.15e+01 ... (remaining 33523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 12784 17.47 - 34.94: 1309 34.94 - 52.40: 507 52.40 - 69.87: 72 69.87 - 87.34: 56 Dihedral angle restraints: 14728 sinusoidal: 5784 harmonic: 8944 Sorted by residual: dihedral pdb=" CA ILE G 398 " pdb=" CB ILE G 398 " pdb=" CG1 ILE G 398 " pdb=" CD1 ILE G 398 " ideal model delta sinusoidal sigma weight residual 60.00 117.31 -57.31 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA ILE E 398 " pdb=" CB ILE E 398 " pdb=" CG1 ILE E 398 " pdb=" CD1 ILE E 398 " ideal model delta sinusoidal sigma weight residual 60.00 117.31 -57.31 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA ILE B 398 " pdb=" CB ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CD1 ILE B 398 " ideal model delta sinusoidal sigma weight residual 60.00 117.29 -57.29 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 14725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3281 0.072 - 0.143: 413 0.143 - 0.215: 2 0.215 - 0.286: 0 0.286 - 0.358: 8 Chirality restraints: 3704 Sorted by residual: chirality pdb=" CA 97U D 503 " pdb=" N 97U D 503 " pdb=" C 97U D 503 " pdb=" CB 97U D 503 " both_signs ideal model delta sigma weight residual False 2.30 2.66 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA 97U H 503 " pdb=" N 97U H 503 " pdb=" C 97U H 503 " pdb=" CB 97U H 503 " both_signs ideal model delta sigma weight residual False 2.30 2.66 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA 97U F 503 " pdb=" N 97U F 503 " pdb=" C 97U F 503 " pdb=" CB 97U F 503 " both_signs ideal model delta sigma weight residual False 2.30 2.66 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3701 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 270 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.86e+00 pdb=" C GLU F 270 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU F 270 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS F 271 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 270 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C GLU B 270 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU B 270 " -0.009 2.00e-02 2.50e+03 pdb=" N HIS B 271 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 270 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C GLU A 270 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU A 270 " -0.009 2.00e-02 2.50e+03 pdb=" N HIS A 271 " -0.008 2.00e-02 2.50e+03 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 51 2.16 - 2.85: 8532 2.85 - 3.53: 33131 3.53 - 4.22: 59324 4.22 - 4.90: 105579 Nonbonded interactions: 206617 Sorted by model distance: nonbonded pdb=" ND1 HIS B 135 " pdb=" OD1 ASP F 105 " model vdw 1.481 3.120 nonbonded pdb=" OD1 ASP D 105 " pdb=" ND1 HIS G 135 " model vdw 1.506 3.120 nonbonded pdb=" OD1 ASP C 105 " pdb=" ND1 HIS H 135 " model vdw 1.530 3.120 nonbonded pdb=" OD1 ASP A 105 " pdb=" ND1 HIS E 135 " model vdw 1.655 3.120 nonbonded pdb=" ND1 HIS D 135 " pdb=" OD1 ASP G 105 " model vdw 1.663 3.120 ... (remaining 206612 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: 0.08 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 24.890 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 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 : 0.008 0.356 24744 Z= 0.370 Angle : 0.589 7.358 33544 Z= 0.323 Chirality : 0.045 0.358 3704 Planarity : 0.003 0.024 4440 Dihedral : 17.223 87.339 9040 Min Nonbonded Distance : 1.481 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.66 % Allowed : 14.92 % Favored : 84.43 % 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: 0.19 (0.15), residues: 3136 helix: 1.38 (0.15), residues: 1288 sheet: 0.31 (0.29), residues: 296 loop : -1.01 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 281 TYR 0.010 0.001 TYR H 88 PHE 0.008 0.001 PHE E 229 TRP 0.006 0.001 TRP G 289 HIS 0.006 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.30 (24704) covalent geometry : angle 0.58940 / 0.32 (33528) SS BOND : bond 0.00123 / 0.06 ( 8) SS BOND : angle 0.40595 / 0.24 ( 16) hydrogen bonds : bond 0.16990 / 11.37 ( 1016) hydrogen bonds : angle 6.29810 / 4.57 ( 2832) metal coordination : bond 0.17776 / 12.60 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 431 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 53 GLN cc_start: 0.5540 (tt0) cc_final: 0.5263 (mm-40) REVERT: A 327 ASP cc_start: 0.5879 (m-30) cc_final: 0.5382 (t70) REVERT: C 115 GLU cc_start: 0.7201 (tt0) cc_final: 0.6962 (tt0) REVERT: D 88 TYR cc_start: 0.6311 (OUTLIER) cc_final: 0.5978 (t80) REVERT: D 281 ARG cc_start: 0.6851 (ttp-170) cc_final: 0.6025 (ttp80) REVERT: E 93 GLN cc_start: 0.7050 (mp10) cc_final: 0.6663 (mm-40) REVERT: E 172 ASP cc_start: 0.7445 (m-30) cc_final: 0.7056 (t0) REVERT: F 88 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5583 (t80) REVERT: F 115 GLU cc_start: 0.7555 (tt0) cc_final: 0.7262 (tt0) REVERT: F 281 ARG cc_start: 0.7250 (ttp-170) cc_final: 0.6776 (ttp-110) REVERT: G 93 GLN cc_start: 0.7103 (mp10) cc_final: 0.6689 (mm-40) REVERT: G 115 GLU cc_start: 0.6549 (tt0) cc_final: 0.5968 (tm-30) REVERT: G 232 ASP cc_start: 0.7196 (m-30) cc_final: 0.6947 (m-30) REVERT: G 281 ARG cc_start: 0.6406 (ttp-170) cc_final: 0.5998 (tmm160) REVERT: H 88 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.5553 (t80) REVERT: H 115 GLU cc_start: 0.7033 (tt0) cc_final: 0.6317 (tm-30) REVERT: H 185 GLU cc_start: 0.7842 (mp0) cc_final: 0.7582 (mp0) REVERT: H 281 ARG cc_start: 0.7207 (ttp-170) cc_final: 0.6729 (ttp-110) outliers start: 16 outliers final: 1 residues processed: 439 average time/residue: 0.6386 time to fit residues: 322.8563 Evaluate side-chains 272 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 268 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain F residue 88 TYR Chi-restraints excluded: chain H residue 88 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.0270 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B 353 ASN A 26 HIS ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN D 26 HIS ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN E 26 HIS ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 ASN F 26 HIS ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN G 26 HIS G 135 HIS ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 HIS G 372 GLN H 26 HIS ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 GLN ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 286 HIS ** H 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.182155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157976 restraints weight = 23260.064| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.23 r_work: 0.3661 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 24744 Z= 0.179 Angle : 0.624 11.794 33544 Z= 0.321 Chirality : 0.047 0.230 3704 Planarity : 0.005 0.089 4440 Dihedral : 8.544 57.085 3729 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.73 % Allowed : 17.13 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.14), residues: 3136 helix: 1.20 (0.14), residues: 1232 sheet: 0.53 (0.31), residues: 304 loop : -0.87 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 47 TYR 0.017 0.002 TYR E 88 PHE 0.026 0.002 PHE D 106 TRP 0.011 0.001 TRP G 79 HIS 0.017 0.002 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (24704) covalent geometry : angle 0.62449 / 0.32 (33528) SS BOND : bond 0.00249 / 0.15 ( 8) SS BOND : angle 0.59240 / 0.32 ( 16) hydrogen bonds : bond 0.03447 / 2.34 ( 1016) hydrogen bonds : angle 4.40682 / 3.18 ( 2832) metal coordination : bond 0.02676 / 1.32 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 365 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.6065 (tt0) cc_final: 0.5826 (mm-40) REVERT: A 71 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6161 (mmm160) REVERT: C 276 THR cc_start: 0.7844 (p) cc_final: 0.7342 (p) REVERT: C 280 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.5576 (mpp) REVERT: D 281 ARG cc_start: 0.7386 (ttp-170) cc_final: 0.7145 (ttp80) REVERT: D 334 ARG cc_start: 0.7701 (ptp-110) cc_final: 0.7358 (ptp90) REVERT: F 70 LEU cc_start: 0.6813 (mt) cc_final: 0.6607 (tp) REVERT: F 71 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.5280 (mmt180) REVERT: F 259 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8323 (mtpp) REVERT: F 281 ARG cc_start: 0.7513 (ttp-170) cc_final: 0.7286 (ttp-110) REVERT: G 131 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: G 281 ARG cc_start: 0.7144 (ttp-170) cc_final: 0.6686 (tmm160) REVERT: H 71 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5034 (mmp-170) REVERT: H 192 ASP cc_start: 0.7866 (m-30) cc_final: 0.7662 (m-30) REVERT: H 259 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8281 (mtpp) REVERT: H 281 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.7247 (ttp-110) outliers start: 91 outliers final: 20 residues processed: 425 average time/residue: 0.6599 time to fit residues: 320.6793 Evaluate side-chains 290 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 412 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 223 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN C 242 ASN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN D 53 GLN D 93 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 HIS ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 326 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.162645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139286 restraints weight = 23744.840| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.19 r_work: 0.3498 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24744 Z= 0.124 Angle : 0.514 9.839 33544 Z= 0.265 Chirality : 0.044 0.214 3704 Planarity : 0.004 0.043 4440 Dihedral : 7.722 57.927 3720 Min Nonbonded Distance : 1.516 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.91 % Allowed : 18.11 % Favored : 78.98 % 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: 0.27 (0.14), residues: 3136 helix: 1.21 (0.14), residues: 1320 sheet: 0.36 (0.29), residues: 304 loop : -0.77 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 37 TYR 0.024 0.001 TYR F 88 PHE 0.021 0.001 PHE B 122 TRP 0.006 0.001 TRP F 79 HIS 0.012 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (24704) covalent geometry : angle 0.51432 / 0.26 (33528) SS BOND : bond 0.00140 / 0.08 ( 8) SS BOND : angle 0.50743 / 0.26 ( 16) hydrogen bonds : bond 0.03092 / 2.11 ( 1016) hydrogen bonds : angle 3.99812 / 2.92 ( 2832) metal coordination : bond 0.01588 / 0.78 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 321 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.6673 (tt0) cc_final: 0.6243 (mm-40) REVERT: A 89 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: A 172 ASP cc_start: 0.8102 (m-30) cc_final: 0.7775 (m-30) REVERT: A 281 ARG cc_start: 0.7282 (ttp-170) cc_final: 0.6956 (ttp80) REVERT: C 89 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: C 172 ASP cc_start: 0.8114 (m-30) cc_final: 0.7797 (m-30) REVERT: C 362 GLU cc_start: 0.6491 (tt0) cc_final: 0.6175 (mm-30) REVERT: C 423 GLU cc_start: 0.6690 (pt0) cc_final: 0.6024 (pm20) REVERT: D 281 ARG cc_start: 0.7407 (ttp-170) cc_final: 0.7096 (ttp80) REVERT: D 334 ARG cc_start: 0.7745 (ptp-110) cc_final: 0.7421 (ptp90) REVERT: D 427 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6688 (mp10) REVERT: E 70 LEU cc_start: 0.5112 (OUTLIER) cc_final: 0.4762 (mt) REVERT: E 172 ASP cc_start: 0.8018 (m-30) cc_final: 0.7596 (t0) REVERT: F 71 ARG cc_start: 0.6868 (mtp85) cc_final: 0.5478 (mmp-170) REVERT: F 89 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: F 259 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8111 (mtpp) REVERT: F 281 ARG cc_start: 0.7528 (ttp-170) cc_final: 0.7165 (ttp-110) REVERT: G 259 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7795 (mttt) REVERT: G 281 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6739 (ttp80) REVERT: G 401 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7950 (mtm) REVERT: H 71 ARG cc_start: 0.6649 (mtp85) cc_final: 0.5310 (mmt180) REVERT: H 131 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7259 (mm-30) REVERT: H 192 ASP cc_start: 0.8242 (m-30) cc_final: 0.8024 (m-30) REVERT: H 281 ARG cc_start: 0.7569 (ttp-170) cc_final: 0.7195 (ttp-110) REVERT: H 326 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: H 391 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7645 (mt-10) outliers start: 71 outliers final: 24 residues processed: 365 average time/residue: 0.6896 time to fit residues: 287.1445 Evaluate side-chains 301 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 427 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 401 MET Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 326 GLN Chi-restraints excluded: chain H residue 412 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 204 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 308 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 266 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 GLN ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN D 326 GLN ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 HIS G 350 HIS ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 326 GLN H 387 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110792 restraints weight = 23425.130| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.29 r_work: 0.3042 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.8409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24744 Z= 0.198 Angle : 0.607 9.722 33544 Z= 0.312 Chirality : 0.047 0.218 3704 Planarity : 0.004 0.040 4440 Dihedral : 7.644 59.737 3720 Min Nonbonded Distance : 1.498 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.24 % Allowed : 18.81 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3136 helix: 1.31 (0.14), residues: 1248 sheet: 0.12 (0.28), residues: 288 loop : -0.79 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 137 TYR 0.022 0.002 TYR F 88 PHE 0.025 0.002 PHE B 122 TRP 0.006 0.001 TRP D 170 HIS 0.008 0.002 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (24704) covalent geometry : angle 0.60715 / 0.31 (33528) SS BOND : bond 0.00320 / 0.14 ( 8) SS BOND : angle 0.73724 / 0.44 ( 16) hydrogen bonds : bond 0.03285 / 2.25 ( 1016) hydrogen bonds : angle 4.28488 / 3.11 ( 2832) metal coordination : bond 0.01393 / 0.70 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 304 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: B 172 ASP cc_start: 0.8071 (m-30) cc_final: 0.7549 (m-30) REVERT: B 281 ARG cc_start: 0.7262 (ttp-170) cc_final: 0.6968 (ttp80) REVERT: A 32 ASP cc_start: 0.7438 (t0) cc_final: 0.7197 (t0) REVERT: A 34 ARG cc_start: 0.8555 (tpt170) cc_final: 0.8154 (mpt180) REVERT: A 172 ASP cc_start: 0.8225 (m-30) cc_final: 0.7672 (m-30) REVERT: A 281 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.6737 (ttp80) REVERT: A 320 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7248 (ttm170) REVERT: C 53 GLN cc_start: 0.7114 (mp10) cc_final: 0.6756 (mt0) REVERT: C 172 ASP cc_start: 0.8129 (m-30) cc_final: 0.7664 (m-30) REVERT: C 280 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7826 (mtt) REVERT: C 362 GLU cc_start: 0.7401 (tt0) cc_final: 0.6859 (mm-30) REVERT: C 423 GLU cc_start: 0.7180 (pt0) cc_final: 0.6574 (tt0) REVERT: D 55 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7130 (pt) REVERT: D 281 ARG cc_start: 0.7412 (ttp-170) cc_final: 0.6794 (ttp80) REVERT: D 334 ARG cc_start: 0.7793 (ptp-110) cc_final: 0.7435 (ptp90) REVERT: D 423 GLU cc_start: 0.7291 (pt0) cc_final: 0.7020 (tt0) REVERT: E 70 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5612 (mt) REVERT: E 71 ARG cc_start: 0.6320 (mtp85) cc_final: 0.4698 (mmt180) REVERT: E 312 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6931 (mm-30) REVERT: E 334 ARG cc_start: 0.7522 (mtm110) cc_final: 0.7301 (ptt-90) REVERT: E 391 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7761 (pt0) REVERT: F 71 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.5587 (mmp80) REVERT: F 89 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: F 131 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7643 (mm-30) REVERT: F 259 LYS cc_start: 0.8283 (ttmt) cc_final: 0.8014 (mtpp) REVERT: F 281 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.6644 (ttp-110) REVERT: G 263 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8008 (mt) REVERT: G 281 ARG cc_start: 0.7418 (mtp180) cc_final: 0.6813 (ttp80) REVERT: G 391 GLU cc_start: 0.7592 (pt0) cc_final: 0.7299 (pt0) REVERT: G 419 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8458 (ttt) REVERT: H 41 PRO cc_start: 0.8226 (Cg_exo) cc_final: 0.7906 (Cg_endo) REVERT: H 71 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.5527 (mmt180) REVERT: H 131 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7618 (mm-30) REVERT: H 281 ARG cc_start: 0.7371 (ttp-170) cc_final: 0.6682 (ttp-110) REVERT: H 307 ASP cc_start: 0.8319 (t70) cc_final: 0.8076 (t70) REVERT: H 326 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7440 (tp40) REVERT: H 391 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7948 (mt-10) outliers start: 79 outliers final: 23 residues processed: 354 average time/residue: 0.7649 time to fit residues: 304.6613 Evaluate side-chains 277 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 419 MET Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 326 GLN Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 412 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 284 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 179 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN C 353 ASN D 53 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 372 GLN ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112722 restraints weight = 23140.986| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.25 r_work: 0.3208 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.8521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24744 Z= 0.122 Angle : 0.512 9.079 33544 Z= 0.260 Chirality : 0.044 0.212 3704 Planarity : 0.003 0.035 4440 Dihedral : 7.237 58.640 3720 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.54 % Allowed : 21.07 % Favored : 76.39 % 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: 0.45 (0.14), residues: 3136 helix: 1.56 (0.14), residues: 1264 sheet: 0.02 (0.31), residues: 256 loop : -0.67 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.016 0.001 TYR D 88 PHE 0.015 0.001 PHE B 122 TRP 0.008 0.001 TRP A 79 HIS 0.016 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (24704) covalent geometry : angle 0.51213 / 0.26 (33528) SS BOND : bond 0.00139 / 0.06 ( 8) SS BOND : angle 0.35405 / 0.20 ( 16) hydrogen bonds : bond 0.02726 / 1.87 ( 1016) hydrogen bonds : angle 4.05218 / 2.95 ( 2832) metal coordination : bond 0.01874 / 0.92 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 276 time to evaluate : 0.880 Fit side-chains REVERT: B 29 LYS cc_start: 0.7150 (mtmm) cc_final: 0.6810 (mtpp) REVERT: B 362 GLU cc_start: 0.6408 (tt0) cc_final: 0.6065 (mm-30) REVERT: A 34 ARG cc_start: 0.8478 (tpt170) cc_final: 0.8165 (mpt180) REVERT: A 172 ASP cc_start: 0.8128 (m-30) cc_final: 0.7628 (m-30) REVERT: A 281 ARG cc_start: 0.7379 (mtp180) cc_final: 0.7021 (ttp80) REVERT: A 320 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.7512 (ttm170) REVERT: C 48 ASP cc_start: 0.8128 (m-30) cc_final: 0.7838 (m-30) REVERT: C 53 GLN cc_start: 0.7298 (mp10) cc_final: 0.7035 (mt0) REVERT: C 172 ASP cc_start: 0.8099 (m-30) cc_final: 0.7681 (m-30) REVERT: C 280 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.6985 (mpp) REVERT: C 281 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7834 (ttp80) REVERT: C 362 GLU cc_start: 0.7334 (tt0) cc_final: 0.6986 (mm-30) REVERT: C 419 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7346 (ttt) REVERT: C 423 GLU cc_start: 0.7028 (pt0) cc_final: 0.6680 (tt0) REVERT: D 47 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7528 (mtt90) REVERT: D 281 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.7066 (ttp80) REVERT: D 334 ARG cc_start: 0.7841 (ptp-110) cc_final: 0.7473 (ptp90) REVERT: E 71 ARG cc_start: 0.6511 (mtp85) cc_final: 0.5149 (mmp-170) REVERT: E 185 GLU cc_start: 0.8823 (mp0) cc_final: 0.8253 (mp0) REVERT: F 71 ARG cc_start: 0.7275 (mtp85) cc_final: 0.6001 (mmp-170) REVERT: F 259 LYS cc_start: 0.8473 (ttmt) cc_final: 0.8214 (mtpp) REVERT: F 281 ARG cc_start: 0.7439 (ttp-170) cc_final: 0.6947 (ttp-110) REVERT: G 185 GLU cc_start: 0.8838 (mp0) cc_final: 0.8292 (mp0) REVERT: G 259 LYS cc_start: 0.8380 (ttmm) cc_final: 0.7810 (mttt) REVERT: G 281 ARG cc_start: 0.7512 (mtp180) cc_final: 0.7049 (ttp80) REVERT: H 41 PRO cc_start: 0.8304 (Cg_exo) cc_final: 0.8047 (Cg_endo) REVERT: H 71 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.5890 (mmt180) REVERT: H 89 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: H 281 ARG cc_start: 0.7521 (ttp-170) cc_final: 0.6982 (ttp-110) REVERT: H 307 ASP cc_start: 0.8289 (t70) cc_final: 0.7628 (m-30) REVERT: H 391 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8118 (mt-10) outliers start: 62 outliers final: 19 residues processed: 315 average time/residue: 0.7663 time to fit residues: 271.9908 Evaluate side-chains 273 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 412 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 161 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 275 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 304 optimal weight: 7.9990 chunk 257 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 271 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN B 242 ASN ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN D 286 HIS ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 GLN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN E 326 GLN E 372 GLN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 GLN ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 326 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.106986 restraints weight = 22896.945| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.26 r_work: 0.3130 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.8947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24744 Z= 0.170 Angle : 0.552 9.145 33544 Z= 0.281 Chirality : 0.046 0.213 3704 Planarity : 0.004 0.040 4440 Dihedral : 7.506 59.764 3720 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.62 % Allowed : 21.07 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3136 helix: 1.49 (0.14), residues: 1256 sheet: -0.05 (0.31), residues: 248 loop : -0.73 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.016 0.002 TYR F 88 PHE 0.019 0.001 PHE B 122 TRP 0.006 0.001 TRP A 79 HIS 0.016 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (24704) covalent geometry : angle 0.55229 / 0.28 (33528) SS BOND : bond 0.00289 / 0.15 ( 8) SS BOND : angle 0.72828 / 0.42 ( 16) hydrogen bonds : bond 0.02983 / 2.04 ( 1016) hydrogen bonds : angle 4.16970 / 3.04 ( 2832) metal coordination : bond 0.01516 / 0.75 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 243 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7362 (mtpt) REVERT: B 53 GLN cc_start: 0.7209 (mp-120) cc_final: 0.6837 (mt0) REVERT: B 172 ASP cc_start: 0.8011 (m-30) cc_final: 0.7550 (m-30) REVERT: B 280 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.6464 (mpp) REVERT: B 302 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: B 307 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: B 362 GLU cc_start: 0.7030 (tt0) cc_final: 0.6706 (mm-30) REVERT: A 32 ASP cc_start: 0.7933 (t0) cc_final: 0.7491 (t70) REVERT: A 172 ASP cc_start: 0.8171 (m-30) cc_final: 0.7728 (m-30) REVERT: A 281 ARG cc_start: 0.7503 (mtp180) cc_final: 0.7126 (ttp80) REVERT: A 320 ARG cc_start: 0.8213 (ttt-90) cc_final: 0.7398 (ttm170) REVERT: C 34 ARG cc_start: 0.8879 (ttm170) cc_final: 0.8454 (tpt170) REVERT: C 53 GLN cc_start: 0.7569 (mp10) cc_final: 0.7128 (mt0) REVERT: C 172 ASP cc_start: 0.8110 (m-30) cc_final: 0.7732 (m-30) REVERT: C 280 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.6912 (mpp) REVERT: C 362 GLU cc_start: 0.7473 (tt0) cc_final: 0.6970 (mm-30) REVERT: C 419 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7355 (ttt) REVERT: C 423 GLU cc_start: 0.7009 (pt0) cc_final: 0.6776 (tt0) REVERT: D 32 ASP cc_start: 0.7997 (t0) cc_final: 0.7768 (t70) REVERT: D 47 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7648 (mtt90) REVERT: D 281 ARG cc_start: 0.7548 (ttp-170) cc_final: 0.7109 (ttp80) REVERT: D 334 ARG cc_start: 0.7872 (ptp-110) cc_final: 0.7524 (ptp90) REVERT: E 41 PRO cc_start: 0.7847 (Cg_exo) cc_final: 0.7539 (Cg_endo) REVERT: E 71 ARG cc_start: 0.7009 (mtp85) cc_final: 0.5451 (mmt180) REVERT: E 380 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8360 (mt-10) REVERT: F 71 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6016 (mmt180) REVERT: F 89 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7538 (tt0) REVERT: F 259 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8214 (mtpp) REVERT: F 281 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.6920 (ttp-110) REVERT: G 71 ARG cc_start: 0.6783 (mtp85) cc_final: 0.5508 (mmp-170) REVERT: G 281 ARG cc_start: 0.7580 (mtp180) cc_final: 0.7110 (ttp80) REVERT: H 41 PRO cc_start: 0.8406 (Cg_exo) cc_final: 0.8155 (Cg_endo) REVERT: H 71 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6155 (mmp-170) REVERT: H 89 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: H 281 ARG cc_start: 0.7552 (ttp-170) cc_final: 0.7006 (ttp-110) REVERT: H 307 ASP cc_start: 0.8401 (t70) cc_final: 0.7831 (m-30) REVERT: H 326 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7784 (mt0) outliers start: 64 outliers final: 24 residues processed: 281 average time/residue: 0.7541 time to fit residues: 239.9231 Evaluate side-chains 266 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain E residue 380 GLU Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 326 GLN Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 412 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 81 optimal weight: 0.0770 chunk 253 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN E 326 GLN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 GLN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 GLN G 372 GLN ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108165 restraints weight = 22804.374| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.22 r_work: 0.3186 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.9067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24744 Z= 0.143 Angle : 0.522 8.437 33544 Z= 0.264 Chirality : 0.045 0.213 3704 Planarity : 0.003 0.044 4440 Dihedral : 7.338 59.999 3720 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.09 % Allowed : 21.80 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3136 helix: 1.58 (0.15), residues: 1256 sheet: -0.15 (0.32), residues: 248 loop : -0.73 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 281 TYR 0.014 0.001 TYR A 88 PHE 0.015 0.001 PHE B 122 TRP 0.006 0.001 TRP D 79 HIS 0.015 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (24704) covalent geometry : angle 0.52208 / 0.26 (33528) SS BOND : bond 0.00221 / 0.13 ( 8) SS BOND : angle 0.56451 / 0.32 ( 16) hydrogen bonds : bond 0.02777 / 1.91 ( 1016) hydrogen bonds : angle 4.10042 / 2.99 ( 2832) metal coordination : bond 0.01431 / 0.70 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7740 (p) REVERT: B 29 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7572 (mtpt) REVERT: B 53 GLN cc_start: 0.7382 (mp-120) cc_final: 0.7048 (mt0) REVERT: B 172 ASP cc_start: 0.7995 (m-30) cc_final: 0.7670 (m-30) REVERT: B 302 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: B 307 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: B 362 GLU cc_start: 0.7037 (tt0) cc_final: 0.6730 (mm-30) REVERT: B 419 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7538 (ttt) REVERT: A 32 ASP cc_start: 0.7915 (t0) cc_final: 0.7428 (t70) REVERT: A 172 ASP cc_start: 0.8135 (m-30) cc_final: 0.7682 (m-30) REVERT: A 281 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7124 (ttp80) REVERT: A 320 ARG cc_start: 0.8193 (ttt-90) cc_final: 0.7404 (ttm170) REVERT: C 32 ASP cc_start: 0.7953 (t0) cc_final: 0.7663 (t70) REVERT: C 47 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7586 (mtt90) REVERT: C 53 GLN cc_start: 0.7589 (mp10) cc_final: 0.7200 (mt0) REVERT: C 172 ASP cc_start: 0.8069 (m-30) cc_final: 0.7671 (m-30) REVERT: C 362 GLU cc_start: 0.7432 (tt0) cc_final: 0.6970 (mm-30) REVERT: D 47 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7742 (mtt90) REVERT: D 281 ARG cc_start: 0.7557 (ttp-170) cc_final: 0.7073 (ttp80) REVERT: D 334 ARG cc_start: 0.7859 (ptp-110) cc_final: 0.7519 (ptp90) REVERT: D 345 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7939 (tpt) REVERT: E 41 PRO cc_start: 0.8015 (Cg_exo) cc_final: 0.7695 (Cg_endo) REVERT: E 71 ARG cc_start: 0.7123 (mtp85) cc_final: 0.5674 (mmt180) REVERT: E 185 GLU cc_start: 0.8861 (mp0) cc_final: 0.8233 (mp0) REVERT: E 326 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: F 71 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6178 (mmt180) REVERT: F 259 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8197 (mtpp) REVERT: F 281 ARG cc_start: 0.7420 (ttp-170) cc_final: 0.6775 (ttp-110) REVERT: G 71 ARG cc_start: 0.6932 (mtp85) cc_final: 0.5632 (mmt180) REVERT: G 281 ARG cc_start: 0.7545 (mtp180) cc_final: 0.7019 (ttp80) REVERT: H 41 PRO cc_start: 0.8458 (Cg_exo) cc_final: 0.8224 (Cg_endo) REVERT: H 71 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6154 (mmp-170) REVERT: H 89 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: H 281 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.6951 (ttp-110) REVERT: H 307 ASP cc_start: 0.8335 (t70) cc_final: 0.7840 (m-30) outliers start: 51 outliers final: 24 residues processed: 275 average time/residue: 0.8049 time to fit residues: 248.9814 Evaluate side-chains 261 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain E residue 326 GLN Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 412 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 183 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS C 326 GLN C 372 GLN D 53 GLN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN F 410 ASN ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 GLN ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113308 restraints weight = 20930.324| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.16 r_work: 0.3026 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.9503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 24744 Z= 0.322 Angle : 0.674 8.208 33544 Z= 0.346 Chirality : 0.051 0.221 3704 Planarity : 0.005 0.051 4440 Dihedral : 8.066 59.889 3720 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.25 % Allowed : 22.09 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.23 (0.14), residues: 3136 helix: 0.84 (0.14), residues: 1288 sheet: -0.46 (0.30), residues: 280 loop : -0.92 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 281 TYR 0.020 0.002 TYR G 274 PHE 0.024 0.002 PHE D 122 TRP 0.008 0.002 TRP F 170 HIS 0.016 0.002 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.32 (24704) covalent geometry : angle 0.67342 / 0.35 (33528) SS BOND : bond 0.00513 / 0.27 ( 8) SS BOND : angle 1.62817 / 0.94 ( 16) hydrogen bonds : bond 0.03774 / 2.56 ( 1016) hydrogen bonds : angle 4.59841 / 3.33 ( 2832) metal coordination : bond 0.01876 / 0.94 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7834 (p) REVERT: B 29 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7532 (mtmt) REVERT: B 53 GLN cc_start: 0.7381 (mp10) cc_final: 0.7018 (mt0) REVERT: B 172 ASP cc_start: 0.8147 (m-30) cc_final: 0.7930 (m-30) REVERT: B 280 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.6858 (mpp) REVERT: B 307 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: B 362 GLU cc_start: 0.7565 (tt0) cc_final: 0.6829 (mm-30) REVERT: B 401 MET cc_start: 0.8486 (mtm) cc_final: 0.8213 (mtm) REVERT: B 419 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7621 (ttt) REVERT: A 32 ASP cc_start: 0.7702 (t0) cc_final: 0.7463 (t0) REVERT: A 50 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7541 (mtt180) REVERT: A 281 ARG cc_start: 0.7314 (mtp180) cc_final: 0.6734 (ttp80) REVERT: C 32 ASP cc_start: 0.7981 (t0) cc_final: 0.7651 (t70) REVERT: C 47 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7452 (mtt90) REVERT: C 50 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7557 (mtt180) REVERT: C 53 GLN cc_start: 0.7468 (mp10) cc_final: 0.7009 (mt0) REVERT: C 362 GLU cc_start: 0.7485 (tt0) cc_final: 0.6689 (mm-30) REVERT: D 47 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7561 (mtt90) REVERT: D 50 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7522 (mtt180) REVERT: D 281 ARG cc_start: 0.7440 (ttp-170) cc_final: 0.6884 (ttp80) REVERT: D 334 ARG cc_start: 0.7891 (ptp-110) cc_final: 0.7685 (ptp90) REVERT: E 47 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7323 (ttp-110) REVERT: E 71 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.5826 (mmt180) REVERT: E 280 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.6478 (mpp) REVERT: F 71 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6018 (mmt180) REVERT: F 259 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7929 (mtpp) REVERT: F 281 ARG cc_start: 0.7332 (ttp-170) cc_final: 0.6605 (ttp-110) REVERT: G 41 PRO cc_start: 0.8121 (Cg_exo) cc_final: 0.7889 (Cg_endo) REVERT: G 71 ARG cc_start: 0.7546 (mtp85) cc_final: 0.5900 (mmp-170) REVERT: G 281 ARG cc_start: 0.7533 (mtp180) cc_final: 0.6802 (ttp80) REVERT: H 41 PRO cc_start: 0.8358 (Cg_exo) cc_final: 0.8134 (Cg_endo) REVERT: H 71 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6065 (mmp-170) REVERT: H 89 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: H 281 ARG cc_start: 0.7446 (ttp-170) cc_final: 0.6695 (ttp-110) REVERT: H 391 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8182 (mt-10) outliers start: 55 outliers final: 23 residues processed: 270 average time/residue: 0.8007 time to fit residues: 243.2104 Evaluate side-chains 245 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 280 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 212 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 276 optimal weight: 0.3980 chunk 141 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN D 53 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS E 326 GLN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN F 410 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 GLN ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121240 restraints weight = 21235.860| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.21 r_work: 0.3259 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.9378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24744 Z= 0.108 Angle : 0.508 5.629 33544 Z= 0.259 Chirality : 0.044 0.218 3704 Planarity : 0.004 0.050 4440 Dihedral : 7.349 58.165 3720 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.64 % Allowed : 22.99 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.23 (0.15), residues: 3136 helix: 1.44 (0.15), residues: 1256 sheet: -0.77 (0.29), residues: 296 loop : -0.69 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 34 TYR 0.020 0.001 TYR F 88 PHE 0.013 0.001 PHE B 122 TRP 0.016 0.001 TRP H 79 HIS 0.016 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (24704) covalent geometry : angle 0.50814 / 0.26 (33528) SS BOND : bond 0.00161 / 0.09 ( 8) SS BOND : angle 0.39540 / 0.22 ( 16) hydrogen bonds : bond 0.02651 / 1.83 ( 1016) hydrogen bonds : angle 4.15652 / 3.02 ( 2832) metal coordination : bond 0.01304 / 0.64 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7572 (mp10) cc_final: 0.7184 (mt0) REVERT: B 172 ASP cc_start: 0.7902 (m-30) cc_final: 0.7505 (m-30) REVERT: B 362 GLU cc_start: 0.7256 (tt0) cc_final: 0.6836 (mm-30) REVERT: B 419 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8382 (tmm) REVERT: A 172 ASP cc_start: 0.8129 (m-30) cc_final: 0.7648 (m-30) REVERT: A 281 ARG cc_start: 0.7397 (mtp180) cc_final: 0.6851 (ttp80) REVERT: C 32 ASP cc_start: 0.8047 (t0) cc_final: 0.7728 (t70) REVERT: C 47 ARG cc_start: 0.8013 (mtm-85) cc_final: 0.7651 (mtt90) REVERT: C 53 GLN cc_start: 0.7634 (mp10) cc_final: 0.7246 (mt0) REVERT: C 172 ASP cc_start: 0.8063 (m-30) cc_final: 0.7529 (m-30) REVERT: C 362 GLU cc_start: 0.7402 (tt0) cc_final: 0.6865 (mm-30) REVERT: D 47 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7806 (mtt90) REVERT: D 281 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.6982 (ttp80) REVERT: D 334 ARG cc_start: 0.7881 (ptp-110) cc_final: 0.7595 (ptp90) REVERT: E 47 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7396 (ttp-110) REVERT: E 71 ARG cc_start: 0.7370 (mtp85) cc_final: 0.6024 (mmp-170) REVERT: E 185 GLU cc_start: 0.8827 (mp0) cc_final: 0.8214 (mp0) REVERT: F 71 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6116 (mmp-170) REVERT: F 259 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8060 (mtpp) REVERT: F 281 ARG cc_start: 0.7401 (ttp-170) cc_final: 0.6702 (ttp-110) REVERT: G 41 PRO cc_start: 0.8170 (Cg_exo) cc_final: 0.7952 (Cg_endo) REVERT: G 71 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6115 (mmp-170) REVERT: G 281 ARG cc_start: 0.7424 (mtp180) cc_final: 0.6808 (ttp80) REVERT: H 71 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6212 (mmp-170) REVERT: H 89 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: H 281 ARG cc_start: 0.7477 (ttp-170) cc_final: 0.6768 (ttp-110) REVERT: H 307 ASP cc_start: 0.8305 (t70) cc_final: 0.7842 (m-30) outliers start: 40 outliers final: 22 residues processed: 259 average time/residue: 0.7770 time to fit residues: 227.3379 Evaluate side-chains 240 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 182 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 162 optimal weight: 0.4980 chunk 180 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 185 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN D 53 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN E 353 ASN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN F 410 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118554 restraints weight = 21344.784| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.09 r_work: 0.3193 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.9397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24744 Z= 0.155 Angle : 0.534 7.804 33544 Z= 0.271 Chirality : 0.045 0.218 3704 Planarity : 0.004 0.050 4440 Dihedral : 7.398 59.408 3720 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.52 % Allowed : 22.91 % Favored : 75.57 % 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: 0.21 (0.15), residues: 3136 helix: 1.42 (0.14), residues: 1256 sheet: -0.75 (0.29), residues: 296 loop : -0.71 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 34 TYR 0.023 0.002 TYR F 88 PHE 0.015 0.001 PHE B 122 TRP 0.013 0.001 TRP H 79 HIS 0.016 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (24704) covalent geometry : angle 0.53436 / 0.27 (33528) SS BOND : bond 0.00208 / 0.11 ( 8) SS BOND : angle 0.69784 / 0.42 ( 16) hydrogen bonds : bond 0.02853 / 1.96 ( 1016) hydrogen bonds : angle 4.18095 / 3.05 ( 2832) metal coordination : bond 0.01454 / 0.71 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7574 (mtt90) REVERT: B 53 GLN cc_start: 0.7588 (mp10) cc_final: 0.7242 (mt0) REVERT: B 172 ASP cc_start: 0.8101 (m-30) cc_final: 0.7655 (m-30) REVERT: B 362 GLU cc_start: 0.7335 (tt0) cc_final: 0.6866 (mm-30) REVERT: A 172 ASP cc_start: 0.8084 (m-30) cc_final: 0.7633 (m-30) REVERT: A 281 ARG cc_start: 0.7441 (mtp180) cc_final: 0.6923 (ttp80) REVERT: C 32 ASP cc_start: 0.8001 (t0) cc_final: 0.7670 (t70) REVERT: C 47 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7750 (mtt90) REVERT: C 53 GLN cc_start: 0.7667 (mp10) cc_final: 0.7248 (mt0) REVERT: C 172 ASP cc_start: 0.8075 (m-30) cc_final: 0.7591 (m-30) REVERT: C 362 GLU cc_start: 0.7436 (tt0) cc_final: 0.6902 (mm-30) REVERT: C 372 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: D 32 ASP cc_start: 0.8109 (t70) cc_final: 0.7901 (t0) REVERT: D 281 ARG cc_start: 0.7536 (ttp-170) cc_final: 0.7037 (ttp80) REVERT: E 47 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7397 (ttp-110) REVERT: E 71 ARG cc_start: 0.7455 (mtp85) cc_final: 0.6097 (mmp-170) REVERT: E 185 GLU cc_start: 0.8864 (mp0) cc_final: 0.8144 (mp0) REVERT: E 320 ARG cc_start: 0.7969 (tmm160) cc_final: 0.7721 (tmm160) REVERT: F 71 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6281 (mmp-170) REVERT: F 259 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8120 (mtpp) REVERT: F 281 ARG cc_start: 0.7429 (ttp-170) cc_final: 0.6735 (ttp-110) REVERT: G 71 ARG cc_start: 0.7529 (mtp85) cc_final: 0.6008 (mmt180) REVERT: G 281 ARG cc_start: 0.7318 (mtp180) cc_final: 0.6760 (ttp80) REVERT: G 362 GLU cc_start: 0.7775 (tt0) cc_final: 0.7515 (mt-10) REVERT: H 71 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6308 (mmp-170) REVERT: H 89 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: H 281 ARG cc_start: 0.7518 (ttp-170) cc_final: 0.6838 (ttp-110) REVERT: H 307 ASP cc_start: 0.8280 (t70) cc_final: 0.7847 (m-30) REVERT: H 324 GLN cc_start: 0.6148 (tp40) cc_final: 0.5818 (tp40) outliers start: 37 outliers final: 24 residues processed: 249 average time/residue: 0.7685 time to fit residues: 216.4251 Evaluate side-chains 242 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 220 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 282 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 chunk 162 optimal weight: 0.3980 chunk 222 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.139111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118884 restraints weight = 21264.306| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.08 r_work: 0.3197 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.9391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 24744 Z= 0.146 Angle : 0.682 59.196 33544 Z= 0.372 Chirality : 0.046 0.631 3704 Planarity : 0.004 0.049 4440 Dihedral : 7.412 59.251 3720 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.48 % Allowed : 22.95 % Favored : 75.57 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.22 (0.15), residues: 3136 helix: 1.42 (0.14), residues: 1256 sheet: -0.75 (0.29), residues: 296 loop : -0.71 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.019 0.001 TYR F 88 PHE 0.015 0.001 PHE B 122 TRP 0.011 0.001 TRP H 79 HIS 0.016 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (24704) covalent geometry : angle 0.68192 / 0.37 (33528) SS BOND : bond 0.00198 / 0.10 ( 8) SS BOND : angle 0.68628 / 0.41 ( 16) hydrogen bonds : bond 0.02826 / 1.94 ( 1016) hydrogen bonds : angle 4.18320 / 3.05 ( 2832) metal coordination : bond 0.01440 / 0.71 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7929.80 seconds wall clock time: 136 minutes 12.19 seconds (8172.19 seconds total)