Starting phenix.real_space_refine on Fri May 23 13:25:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yak_39101/05_2025/8yak_39101_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yak_39101/05_2025/8yak_39101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yak_39101/05_2025/8yak_39101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yak_39101/05_2025/8yak_39101.map" model { file = "/net/cci-nas-00/data/ceres_data/8yak_39101/05_2025/8yak_39101_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yak_39101/05_2025/8yak_39101_trim.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.064 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 15160 2.51 5 N 4320 2.21 5 O 4632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24216 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2997 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: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2997 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: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2997 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: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2997 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: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2997 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: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2997 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: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2997 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: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2997 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: 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: "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: "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: 13.23, per 1000 atoms: 0.55 Number of scatterers: 24216 At special positions: 0 Unit cell: (126.65, 126.65, 105.4, 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 4632 8.00 N 4320 7.00 C 15160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 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: 5.93 Conformation dependent library (CDL) restraints added in 3.1 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 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " 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: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.743A 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: 3.815A pdb=" N ARG A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.137A 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: 3.694A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.979A 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: 4.121A 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: 3.663A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 removed outlier: 3.520A pdb=" N LEU A 413 " --> pdb=" O ASN A 410 " (cutoff:3.500A) 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: 3.683A 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: 4.120A 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 '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: 3.815A 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: 3.521A 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: 3.682A pdb=" N TYR D 108 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 3.815A 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: 3.695A 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: 3.664A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 414 removed outlier: 3.522A pdb=" N LEU D 413 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.743A pdb=" N PHE E 99 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.683A 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: 4.135A 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: 3.664A 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: 3.681A 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: 4.135A 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: 3.696A 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: 3.662A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 414 removed outlier: 3.523A pdb=" N LEU F 413 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 100 removed outlier: 3.744A 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: 3.814A 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: 3.977A 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: 3.663A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 414 removed outlier: 3.522A 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: 3.683A pdb=" N TYR H 108 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 3.815A 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: 3.978A 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: 4.120A 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: 3.520A pdb=" N LEU H 413 " --> pdb=" O ASN H 410 " (cutoff:3.500A) Processing sheet with id=AA1, 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: 4.237A pdb=" N LEU A 54 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 45 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 39 removed outlier: 13.822A 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: 12.136A pdb=" N LEU A 25 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 10.594A 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: 7.067A 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: 8.774A pdb=" N PHE A 31 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 418 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.318A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.068A 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: 6.879A pdb=" N VAL A 125 " --> pdb=" O PHE A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.503A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 268 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA5, 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: 6.688A pdb=" N VAL B 45 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing sheet with id=AA6, 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: 12.136A 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: 6.683A 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=AA7, 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: 6.953A 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=AA7 Processing sheet with id=AA8, 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=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: 6.687A 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: 13.822A 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: 12.136A 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: 6.043A 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: 8.774A pdb=" N PHE C 31 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.586A 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: 7.068A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR C 123 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N PHE C 151 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.879A 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: 7.784A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 3.647A 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: 6.313A pdb=" N THR D 43 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU D 54 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.688A 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: 10.595A 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: 7.067A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 8.774A 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: 6.259A 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: 6.318A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR D 123 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 8.349A 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: 6.502A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.783A 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: 3.648A 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: 6.313A 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: 6.687A 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: 12.137A 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: 7.067A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.586A 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: 8.286A 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: 6.953A pdb=" N THR E 123 " --> pdb=" O ARG E 149 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N PHE E 151 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.880A 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: 7.783A 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: 6.311A pdb=" N THR F 43 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 4.238A 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: 13.820A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 13.288A 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: 7.067A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.257A 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: 6.318A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR F 123 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N PHE F 151 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.879A 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: 7.784A 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: 4.236A pdb=" N LEU G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.686A 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: 13.822A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 13.285A 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: 7.065A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N PHE G 31 " --> pdb=" O PRO G 77 " (cutoff:3.500A) removed outlier: 3.587A 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: 6.317A 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: 7.070A 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: 6.877A 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: 7.784A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 6.860A 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: 6.311A pdb=" N THR H 43 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.687A 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: 13.820A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 13.287A pdb=" N ARG H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.137A pdb=" N LEU H 25 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N ARG H 73 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N CYS H 27 " --> pdb=" O ARG H 73 " (cutoff:3.500A) removed outlier: 7.065A 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: 8.774A 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: 6.258A 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: 6.318A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 6.953A 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: 6.503A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.784A 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: 3.648A 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: 8.23 Time building geometry restraints manager: 6.87 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: 5118 1.33 - 1.45: 5655 1.45 - 1.57: 13763 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 24688 Sorted by residual: bond pdb=" CB 97U E 503 " pdb=" CG 97U E 503 " ideal model delta sigma weight residual 1.505 1.372 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CB 97U D 503 " pdb=" CG 97U D 503 " ideal model delta sigma weight residual 1.505 1.372 0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" CB 97U A 503 " pdb=" CG 97U A 503 " ideal model delta sigma weight residual 1.505 1.372 0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" CB 97U G 503 " pdb=" CG 97U G 503 " ideal model delta sigma weight residual 1.505 1.373 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" CB 97U H 503 " pdb=" CG 97U H 503 " ideal model delta sigma weight residual 1.505 1.373 0.132 2.00e-02 2.50e+03 4.35e+01 ... (remaining 24683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 33176 2.73 - 5.46: 248 5.46 - 8.18: 56 8.18 - 10.91: 8 10.91 - 13.64: 16 Bond angle restraints: 33504 Sorted by residual: angle pdb=" CA 97U G 503 " pdb=" N 97U G 503 " pdb=" CAN 97U G 503 " ideal model delta sigma weight residual 122.87 136.51 -13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" CA 97U H 503 " pdb=" N 97U H 503 " pdb=" CAN 97U H 503 " ideal model delta sigma weight residual 122.87 136.50 -13.63 3.00e+00 1.11e-01 2.06e+01 angle pdb=" CA 97U D 503 " pdb=" N 97U D 503 " pdb=" CAN 97U D 503 " ideal model delta sigma weight residual 122.87 136.46 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" CA 97U C 503 " pdb=" N 97U C 503 " pdb=" CAN 97U C 503 " ideal model delta sigma weight residual 122.87 136.46 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" CA 97U A 503 " pdb=" N 97U A 503 " pdb=" CAN 97U A 503 " ideal model delta sigma weight residual 122.87 136.43 -13.56 3.00e+00 1.11e-01 2.04e+01 ... (remaining 33499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 12748 17.45 - 34.90: 1353 34.90 - 52.35: 459 52.35 - 69.80: 136 69.80 - 87.25: 40 Dihedral angle restraints: 14736 sinusoidal: 5800 harmonic: 8936 Sorted by residual: 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 60.00 117.42 -57.42 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA ILE A 398 " pdb=" CB ILE A 398 " pdb=" CG1 ILE A 398 " pdb=" CD1 ILE A 398 " ideal model delta sinusoidal sigma weight residual 60.00 117.40 -57.40 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA ILE H 398 " pdb=" CB ILE H 398 " pdb=" CG1 ILE H 398 " pdb=" CD1 ILE H 398 " ideal model delta sinusoidal sigma weight residual 60.00 117.40 -57.40 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 14733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3178 0.063 - 0.126: 503 0.126 - 0.189: 15 0.189 - 0.252: 0 0.252 - 0.315: 16 Chirality restraints: 3712 Sorted by residual: chirality pdb=" CAH 97U H 503 " pdb=" CAG 97U H 503 " pdb=" CAL 97U H 503 " pdb=" OAI 97U H 503 " both_signs ideal model delta sigma weight residual False -2.47 -2.16 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CAH 97U G 503 " pdb=" CAG 97U G 503 " pdb=" CAL 97U G 503 " pdb=" OAI 97U G 503 " both_signs ideal model delta sigma weight residual False -2.47 -2.16 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CAH 97U F 503 " pdb=" CAG 97U F 503 " pdb=" CAL 97U F 503 " pdb=" OAI 97U F 503 " both_signs ideal model delta sigma weight residual False -2.47 -2.16 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 3709 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 270 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C GLU D 270 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU D 270 " -0.009 2.00e-02 2.50e+03 pdb=" N HIS D 271 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 270 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.95e+00 pdb=" C GLU G 270 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU G 270 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS G 271 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 270 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C GLU C 270 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU C 270 " -0.009 2.00e-02 2.50e+03 pdb=" N HIS C 271 " -0.008 2.00e-02 2.50e+03 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 176 2.63 - 3.20: 20822 3.20 - 3.77: 36565 3.77 - 4.33: 55689 4.33 - 4.90: 89861 Nonbonded interactions: 203113 Sorted by model distance: nonbonded pdb=" OQ2 KCX G 210 " pdb="ZN ZN G 502 " model vdw 2.063 2.230 nonbonded pdb=" OQ2 KCX E 210 " pdb="ZN ZN E 502 " model vdw 2.063 2.230 nonbonded pdb=" OQ2 KCX D 210 " pdb="ZN ZN D 502 " model vdw 2.063 2.230 nonbonded pdb=" OQ2 KCX C 210 " pdb="ZN ZN C 502 " model vdw 2.063 2.230 nonbonded pdb=" OQ2 KCX H 210 " pdb="ZN ZN H 502 " model vdw 2.064 2.230 ... (remaining 203108 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 1.670 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: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 56.440 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 : 0.009 0.356 24728 Z= 0.362 Angle : 0.678 13.641 33520 Z= 0.332 Chirality : 0.046 0.315 3712 Planarity : 0.003 0.024 4440 Dihedral : 17.341 87.246 9048 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.33 % Allowed : 14.62 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3136 helix: 1.38 (0.15), residues: 1288 sheet: 0.31 (0.29), residues: 296 loop : -0.95 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 289 HIS 0.007 0.001 HIS B 251 PHE 0.008 0.001 PHE H 229 TYR 0.010 0.001 TYR A 333 ARG 0.002 0.000 ARG F 281 Details of bonding type rmsd hydrogen bonds : bond 0.16984 ( 1016) hydrogen bonds : angle 6.30089 ( 2832) metal coordination : bond 0.17767 ( 32) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.38906 ( 16) covalent geometry : bond 0.00563 (24688) covalent geometry : angle 0.67815 (33504) *********************** 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 487 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 479 time to evaluate : 2.725 Fit side-chains REVERT: A 88 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7684 (t0) REVERT: A 259 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7855 (tttm) REVERT: A 277 ASP cc_start: 0.7832 (m-30) cc_final: 0.7544 (m-30) REVERT: A 281 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.7125 (mtt90) REVERT: A 283 MET cc_start: 0.8916 (mtp) cc_final: 0.8623 (mtp) REVERT: A 360 MET cc_start: 0.8875 (mtp) cc_final: 0.8496 (mtp) REVERT: B 88 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7672 (t0) REVERT: B 259 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7864 (tttm) REVERT: B 277 ASP cc_start: 0.7877 (m-30) cc_final: 0.7586 (m-30) REVERT: B 281 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7125 (mtt90) REVERT: B 283 MET cc_start: 0.8927 (mtp) cc_final: 0.8641 (mtp) REVERT: B 360 MET cc_start: 0.8869 (mtp) cc_final: 0.8466 (mtp) REVERT: C 53 GLN cc_start: 0.7986 (tt0) cc_final: 0.7751 (tt0) REVERT: C 88 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7728 (t0) REVERT: C 259 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7838 (tttm) REVERT: C 277 ASP cc_start: 0.7886 (m-30) cc_final: 0.7618 (m-30) REVERT: C 281 ARG cc_start: 0.7502 (ttp-170) cc_final: 0.7131 (mtt90) REVERT: C 283 MET cc_start: 0.8928 (mtp) cc_final: 0.8663 (mtp) REVERT: D 88 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7722 (t0) REVERT: D 259 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7844 (tttm) REVERT: D 277 ASP cc_start: 0.7895 (m-30) cc_final: 0.7615 (m-30) REVERT: D 281 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.7147 (mtt90) REVERT: D 283 MET cc_start: 0.8920 (mtp) cc_final: 0.8652 (mtp) REVERT: E 259 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7947 (tttt) REVERT: E 278 GLU cc_start: 0.7269 (tt0) cc_final: 0.7025 (pt0) REVERT: G 259 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7943 (tttt) REVERT: G 278 GLU cc_start: 0.7252 (tt0) cc_final: 0.7014 (pt0) REVERT: G 284 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8158 (mtmm) REVERT: H 284 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8160 (mtmm) outliers start: 8 outliers final: 0 residues processed: 479 average time/residue: 1.6103 time to fit residues: 866.7414 Evaluate side-chains 301 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 297 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 88 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 159 optimal weight: 0.0020 chunk 126 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 326 GLN B 26 HIS B 326 GLN C 26 HIS C 326 GLN D 26 HIS D 326 GLN E 26 HIS E 271 HIS E 335 ASN E 344 ASN F 26 HIS F 271 HIS F 335 ASN F 344 ASN G 26 HIS G 271 HIS G 335 ASN G 344 ASN H 26 HIS H 271 HIS H 335 ASN H 344 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096636 restraints weight = 22419.336| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.39 r_work: 0.3158 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.797 24728 Z= 0.401 Angle : 0.615 5.264 33520 Z= 0.330 Chirality : 0.051 0.239 3712 Planarity : 0.005 0.050 4440 Dihedral : 8.336 69.717 3720 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.45 % Allowed : 14.91 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3136 helix: 1.36 (0.15), residues: 1288 sheet: 0.60 (0.30), residues: 296 loop : -1.02 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 289 HIS 0.010 0.002 HIS H 251 PHE 0.014 0.002 PHE D 229 TYR 0.017 0.002 TYR C 333 ARG 0.006 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.06507 ( 1016) hydrogen bonds : angle 4.47889 ( 2832) metal coordination : bond 0.28135 ( 32) SS BOND : bond 0.00266 ( 8) SS BOND : angle 0.58343 ( 16) covalent geometry : bond 0.00519 (24688) covalent geometry : angle 0.61549 (33504) *********************** 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 366 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 306 time to evaluate : 2.499 Fit side-chains REVERT: A 88 ASP cc_start: 0.8254 (p0) cc_final: 0.7853 (t0) REVERT: A 259 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8089 (tttm) REVERT: A 281 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7391 (mtm110) REVERT: B 88 ASP cc_start: 0.8256 (p0) cc_final: 0.7861 (t0) REVERT: B 259 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8073 (tttm) REVERT: B 281 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7402 (mtm110) REVERT: C 88 ASP cc_start: 0.8272 (p0) cc_final: 0.7867 (t0) REVERT: C 259 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8071 (tttm) REVERT: C 281 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7397 (mtt90) REVERT: D 88 ASP cc_start: 0.8280 (p0) cc_final: 0.7857 (t0) REVERT: D 259 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8072 (tttm) REVERT: D 281 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7402 (mtt90) REVERT: E 278 GLU cc_start: 0.7823 (tt0) cc_final: 0.7470 (mp0) REVERT: G 278 GLU cc_start: 0.7838 (tt0) cc_final: 0.7479 (mp0) REVERT: G 284 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8177 (mtpp) REVERT: G 327 ASP cc_start: 0.8103 (m-30) cc_final: 0.7837 (m-30) REVERT: H 284 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8166 (mtpp) REVERT: H 327 ASP cc_start: 0.8102 (m-30) cc_final: 0.7836 (m-30) outliers start: 60 outliers final: 26 residues processed: 342 average time/residue: 1.5766 time to fit residues: 607.1399 Evaluate side-chains 292 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 58 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 230 optimal weight: 0.0970 chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A 326 GLN A 344 ASN B 271 HIS B 326 GLN B 344 ASN C 271 HIS C 326 GLN C 344 ASN D 271 HIS D 326 GLN D 344 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099126 restraints weight = 22037.602| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.43 r_work: 0.3186 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.790 24728 Z= 0.363 Angle : 0.518 4.972 33520 Z= 0.277 Chirality : 0.047 0.229 3712 Planarity : 0.004 0.036 4440 Dihedral : 7.346 56.302 3712 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.72 % Allowed : 15.44 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3136 helix: 1.50 (0.15), residues: 1288 sheet: 0.70 (0.30), residues: 296 loop : -0.99 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 289 HIS 0.007 0.001 HIS F 251 PHE 0.011 0.001 PHE D 229 TYR 0.014 0.002 TYR A 333 ARG 0.004 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 1016) hydrogen bonds : angle 4.15704 ( 2832) metal coordination : bond 0.27900 ( 32) SS BOND : bond 0.00177 ( 8) SS BOND : angle 0.27787 ( 16) covalent geometry : bond 0.00325 (24688) covalent geometry : angle 0.51855 (33504) *********************** 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 331 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 289 time to evaluate : 2.659 Fit side-chains REVERT: A 88 ASP cc_start: 0.8272 (p0) cc_final: 0.7831 (t0) REVERT: A 259 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8024 (tttm) REVERT: A 281 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7351 (mtt90) REVERT: B 88 ASP cc_start: 0.8278 (p0) cc_final: 0.7845 (t0) REVERT: B 259 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8037 (tttm) REVERT: B 281 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7336 (mtt90) REVERT: C 88 ASP cc_start: 0.8286 (p0) cc_final: 0.7857 (t0) REVERT: C 259 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8025 (tttm) REVERT: C 281 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7350 (mtt90) REVERT: D 88 ASP cc_start: 0.8288 (p0) cc_final: 0.7851 (t0) REVERT: D 259 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8029 (tttm) REVERT: D 281 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7353 (mtt90) REVERT: G 278 GLU cc_start: 0.7810 (tt0) cc_final: 0.7388 (mp0) REVERT: G 284 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8175 (mtpp) REVERT: G 325 ILE cc_start: 0.7855 (mm) cc_final: 0.7652 (mm) REVERT: G 327 ASP cc_start: 0.8120 (m-30) cc_final: 0.7877 (m-30) REVERT: H 284 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8182 (mtpp) REVERT: H 325 ILE cc_start: 0.7850 (mm) cc_final: 0.7643 (mm) REVERT: H 327 ASP cc_start: 0.8123 (m-30) cc_final: 0.7882 (m-30) outliers start: 42 outliers final: 27 residues processed: 307 average time/residue: 1.6453 time to fit residues: 568.0424 Evaluate side-chains 310 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 3 optimal weight: 0.0670 chunk 121 optimal weight: 6.9990 chunk 230 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 326 GLN C 326 GLN D 326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099539 restraints weight = 21719.466| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.47 r_work: 0.3198 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 24728 Z= 0.134 Angle : 0.508 5.214 33520 Z= 0.271 Chirality : 0.046 0.225 3712 Planarity : 0.004 0.034 4440 Dihedral : 6.800 52.999 3712 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.37 % Allowed : 14.42 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3136 helix: 1.58 (0.15), residues: 1288 sheet: 0.74 (0.30), residues: 296 loop : -1.00 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS E 251 PHE 0.009 0.001 PHE A 229 TYR 0.014 0.001 TYR A 333 ARG 0.003 0.000 ARG F 50 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 1016) hydrogen bonds : angle 4.04429 ( 2832) metal coordination : bond 0.00255 ( 32) SS BOND : bond 0.00156 ( 8) SS BOND : angle 0.25399 ( 16) covalent geometry : bond 0.00307 (24688) covalent geometry : angle 0.50839 (33504) *********************** 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 345 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 2.610 Fit side-chains REVERT: A 88 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7820 (t0) REVERT: A 259 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8232 (ttpp) REVERT: A 281 ARG cc_start: 0.7698 (ttp-170) cc_final: 0.7354 (mtt90) REVERT: B 88 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7847 (t0) REVERT: B 259 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8197 (ttpp) REVERT: B 281 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7345 (mtt90) REVERT: C 37 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6970 (mtm180) REVERT: C 88 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7861 (t0) REVERT: C 259 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8024 (tttm) REVERT: C 281 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7349 (mtt90) REVERT: D 37 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6995 (mtm180) REVERT: D 88 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7857 (t0) REVERT: D 259 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8033 (tttm) REVERT: D 281 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7356 (mtt90) REVERT: G 278 GLU cc_start: 0.7750 (tt0) cc_final: 0.7356 (mp0) REVERT: G 284 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8180 (mtpp) REVERT: G 327 ASP cc_start: 0.8113 (m-30) cc_final: 0.7873 (m-30) REVERT: H 284 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8184 (mtpp) REVERT: H 327 ASP cc_start: 0.8125 (m-30) cc_final: 0.7886 (m-30) outliers start: 58 outliers final: 26 residues processed: 314 average time/residue: 1.6430 time to fit residues: 578.5981 Evaluate side-chains 309 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 48 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 249 optimal weight: 0.0670 chunk 193 optimal weight: 0.1980 chunk 162 optimal weight: 3.9990 chunk 265 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 326 GLN C 326 GLN D 326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099730 restraints weight = 21076.078| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.46 r_work: 0.3202 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24728 Z= 0.124 Angle : 0.495 6.014 33520 Z= 0.263 Chirality : 0.046 0.226 3712 Planarity : 0.004 0.034 4440 Dihedral : 6.607 53.254 3712 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.96 % Allowed : 14.91 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3136 helix: 1.65 (0.15), residues: 1288 sheet: 0.77 (0.30), residues: 296 loop : -0.98 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 289 HIS 0.007 0.001 HIS E 251 PHE 0.008 0.001 PHE D 229 TYR 0.014 0.001 TYR A 333 ARG 0.003 0.000 ARG F 50 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 1016) hydrogen bonds : angle 3.97578 ( 2832) metal coordination : bond 0.00266 ( 32) SS BOND : bond 0.00131 ( 8) SS BOND : angle 0.20867 ( 16) covalent geometry : bond 0.00283 (24688) covalent geometry : angle 0.49507 (33504) *********************** 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 322 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 274 time to evaluate : 2.467 Fit side-chains REVERT: A 88 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7808 (t0) REVERT: A 259 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8241 (ttpp) REVERT: A 281 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7366 (mtt90) REVERT: B 88 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7814 (t0) REVERT: B 259 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8236 (ttpp) REVERT: B 281 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7360 (mtt90) REVERT: C 88 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7811 (t0) REVERT: C 259 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8014 (tttm) REVERT: C 281 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7356 (mtt90) REVERT: D 88 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7816 (t0) REVERT: D 259 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8023 (tttm) REVERT: D 281 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7365 (mtt90) REVERT: G 278 GLU cc_start: 0.7719 (tt0) cc_final: 0.7334 (mp0) REVERT: G 284 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8175 (mtpp) REVERT: G 327 ASP cc_start: 0.8138 (m-30) cc_final: 0.7909 (m-30) REVERT: H 327 ASP cc_start: 0.8156 (m-30) cc_final: 0.7931 (m-30) outliers start: 48 outliers final: 27 residues processed: 294 average time/residue: 1.6803 time to fit residues: 553.4856 Evaluate side-chains 310 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 228 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 256 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 281 optimal weight: 7.9990 chunk 295 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 326 GLN C 326 GLN D 326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097943 restraints weight = 20489.547| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.42 r_work: 0.3162 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24728 Z= 0.202 Angle : 0.577 6.430 33520 Z= 0.309 Chirality : 0.050 0.232 3712 Planarity : 0.005 0.050 4440 Dihedral : 7.560 55.803 3712 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.49 % Allowed : 14.62 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3136 helix: 1.46 (0.15), residues: 1288 sheet: 0.74 (0.30), residues: 296 loop : -1.08 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.008 0.001 HIS H 251 PHE 0.012 0.002 PHE C 229 TYR 0.017 0.002 TYR A 333 ARG 0.003 0.001 ARG F 50 Details of bonding type rmsd hydrogen bonds : bond 0.05998 ( 1016) hydrogen bonds : angle 4.21726 ( 2832) metal coordination : bond 0.00461 ( 32) SS BOND : bond 0.00172 ( 8) SS BOND : angle 0.27807 ( 16) covalent geometry : bond 0.00483 (24688) covalent geometry : angle 0.57692 (33504) *********************** 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 332 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 2.484 Fit side-chains REVERT: A 88 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7848 (t0) REVERT: A 259 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8014 (tttm) REVERT: A 281 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7372 (mtt90) REVERT: B 88 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7845 (t0) REVERT: B 259 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8031 (tttm) REVERT: B 281 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7371 (mtt90) REVERT: C 88 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7829 (t0) REVERT: C 259 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8035 (tttm) REVERT: C 281 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7363 (mtt90) REVERT: D 88 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7843 (t0) REVERT: D 259 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7991 (tttm) REVERT: D 281 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7374 (mtt90) REVERT: G 278 GLU cc_start: 0.7802 (tt0) cc_final: 0.7388 (mp0) REVERT: G 284 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8167 (mtpp) REVERT: G 327 ASP cc_start: 0.8110 (m-30) cc_final: 0.7874 (m-30) REVERT: H 327 ASP cc_start: 0.8124 (m-30) cc_final: 0.7888 (m-30) outliers start: 61 outliers final: 24 residues processed: 298 average time/residue: 1.6343 time to fit residues: 550.5837 Evaluate side-chains 302 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 35 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098257 restraints weight = 20482.637| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.42 r_work: 0.3177 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24728 Z= 0.186 Angle : 0.564 7.750 33520 Z= 0.301 Chirality : 0.049 0.231 3712 Planarity : 0.005 0.048 4440 Dihedral : 7.442 54.468 3712 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.21 % Allowed : 15.28 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3136 helix: 1.44 (0.15), residues: 1288 sheet: 0.70 (0.30), residues: 296 loop : -1.11 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 289 HIS 0.007 0.001 HIS G 251 PHE 0.011 0.002 PHE G 229 TYR 0.017 0.002 TYR A 333 ARG 0.004 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.05718 ( 1016) hydrogen bonds : angle 4.17806 ( 2832) metal coordination : bond 0.00398 ( 32) SS BOND : bond 0.00172 ( 8) SS BOND : angle 0.26893 ( 16) covalent geometry : bond 0.00443 (24688) covalent geometry : angle 0.56402 (33504) *********************** 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 326 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 2.656 Fit side-chains REVERT: A 88 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7853 (t0) REVERT: A 259 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8026 (tttm) REVERT: A 281 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7383 (mtt90) REVERT: B 88 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7850 (t0) REVERT: B 259 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8016 (tttm) REVERT: B 281 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7380 (mtt90) REVERT: C 88 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7844 (t0) REVERT: C 259 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8039 (tttm) REVERT: C 281 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7389 (mtt90) REVERT: D 88 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7845 (t0) REVERT: D 259 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8015 (tttm) REVERT: D 281 ARG cc_start: 0.7732 (ttp-170) cc_final: 0.7391 (mtt90) REVERT: E 278 GLU cc_start: 0.7789 (tt0) cc_final: 0.7577 (tt0) REVERT: G 278 GLU cc_start: 0.7812 (tt0) cc_final: 0.7395 (mp0) REVERT: G 284 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8159 (mtpp) REVERT: G 327 ASP cc_start: 0.8127 (m-30) cc_final: 0.7894 (m-30) REVERT: H 327 ASP cc_start: 0.8144 (m-30) cc_final: 0.7912 (m-30) outliers start: 54 outliers final: 28 residues processed: 302 average time/residue: 1.6422 time to fit residues: 556.9247 Evaluate side-chains 306 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 252 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 258 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN D 326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099186 restraints weight = 20653.230| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.43 r_work: 0.3188 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24728 Z= 0.151 Angle : 0.529 7.835 33520 Z= 0.281 Chirality : 0.047 0.228 3712 Planarity : 0.004 0.038 4440 Dihedral : 7.068 52.214 3712 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.84 % Allowed : 15.97 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3136 helix: 1.53 (0.15), residues: 1288 sheet: 0.70 (0.30), residues: 296 loop : -1.08 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 289 HIS 0.007 0.001 HIS E 251 PHE 0.009 0.001 PHE C 229 TYR 0.015 0.002 TYR D 333 ARG 0.004 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 1016) hydrogen bonds : angle 4.08533 ( 2832) metal coordination : bond 0.00323 ( 32) SS BOND : bond 0.00136 ( 8) SS BOND : angle 0.21919 ( 16) covalent geometry : bond 0.00353 (24688) covalent geometry : angle 0.52878 (33504) *********************** 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 318 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 2.935 Fit side-chains REVERT: A 88 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7845 (t0) REVERT: A 259 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8008 (tttm) REVERT: A 281 ARG cc_start: 0.7705 (ttp-170) cc_final: 0.7375 (mtt90) REVERT: B 88 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7849 (t0) REVERT: B 259 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8023 (tttm) REVERT: B 281 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7364 (mtt90) REVERT: C 88 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7816 (t0) REVERT: C 259 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8033 (tttm) REVERT: C 281 ARG cc_start: 0.7701 (ttp-170) cc_final: 0.7378 (mtt90) REVERT: D 88 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7822 (t0) REVERT: D 259 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8006 (tttm) REVERT: D 281 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7381 (mtt90) REVERT: E 278 GLU cc_start: 0.7760 (tt0) cc_final: 0.7556 (tt0) REVERT: G 278 GLU cc_start: 0.7816 (tt0) cc_final: 0.7410 (mp0) REVERT: G 284 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8166 (mtpp) REVERT: G 327 ASP cc_start: 0.8133 (m-30) cc_final: 0.7904 (m-30) REVERT: H 327 ASP cc_start: 0.8135 (m-30) cc_final: 0.7911 (m-30) outliers start: 45 outliers final: 28 residues processed: 290 average time/residue: 1.6808 time to fit residues: 546.9042 Evaluate side-chains 306 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 123 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 287 optimal weight: 0.0970 chunk 101 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 201 optimal weight: 0.0030 chunk 58 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 326 GLN C 326 GLN D 326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100436 restraints weight = 21215.486| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.46 r_work: 0.3214 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 24728 Z= 0.109 Angle : 0.483 8.508 33520 Z= 0.254 Chirality : 0.045 0.225 3712 Planarity : 0.004 0.037 4440 Dihedral : 6.358 52.253 3712 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.47 % Allowed : 16.42 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3136 helix: 1.68 (0.15), residues: 1288 sheet: 0.70 (0.29), residues: 296 loop : -1.00 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 289 HIS 0.007 0.001 HIS E 251 PHE 0.007 0.001 PHE C 229 TYR 0.013 0.001 TYR A 333 ARG 0.004 0.000 ARG F 50 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 1016) hydrogen bonds : angle 3.91513 ( 2832) metal coordination : bond 0.00259 ( 32) SS BOND : bond 0.00111 ( 8) SS BOND : angle 0.18481 ( 16) covalent geometry : bond 0.00244 (24688) covalent geometry : angle 0.48327 (33504) *********************** 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 316 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 2.842 Fit side-chains REVERT: A 88 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7816 (t0) REVERT: A 259 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8000 (tttm) REVERT: A 281 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7371 (mtt90) REVERT: B 88 ASP cc_start: 0.8300 (p0) cc_final: 0.7812 (t0) REVERT: B 259 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8002 (tttm) REVERT: B 281 ARG cc_start: 0.7679 (ttp-170) cc_final: 0.7367 (mtt90) REVERT: C 88 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7797 (t0) REVERT: C 259 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8003 (tttm) REVERT: C 281 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7381 (mtt90) REVERT: D 88 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7812 (t0) REVERT: D 259 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8001 (tttm) REVERT: D 281 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7390 (mtt90) REVERT: E 278 GLU cc_start: 0.7681 (tt0) cc_final: 0.7478 (tt0) REVERT: G 278 GLU cc_start: 0.7781 (tt0) cc_final: 0.7363 (mp0) REVERT: G 284 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8177 (mtpp) REVERT: G 327 ASP cc_start: 0.8135 (m-30) cc_final: 0.7931 (m-30) REVERT: H 327 ASP cc_start: 0.8160 (m-30) cc_final: 0.7952 (m-30) outliers start: 36 outliers final: 17 residues processed: 299 average time/residue: 1.7371 time to fit residues: 580.8913 Evaluate side-chains 302 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 278 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 180 optimal weight: 9.9990 chunk 290 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 175 optimal weight: 0.3980 chunk 200 optimal weight: 0.0970 chunk 186 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 326 GLN C 326 GLN D 326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100189 restraints weight = 21146.322| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.46 r_work: 0.3206 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 24728 Z= 0.114 Angle : 0.492 9.552 33520 Z= 0.258 Chirality : 0.045 0.225 3712 Planarity : 0.004 0.037 4440 Dihedral : 6.397 52.954 3712 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.39 % Allowed : 16.63 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3136 helix: 1.69 (0.15), residues: 1288 sheet: 0.72 (0.29), residues: 296 loop : -0.97 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 289 HIS 0.007 0.001 HIS E 251 PHE 0.007 0.001 PHE C 229 TYR 0.013 0.001 TYR D 333 ARG 0.007 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 1016) hydrogen bonds : angle 3.91452 ( 2832) metal coordination : bond 0.00264 ( 32) SS BOND : bond 0.00108 ( 8) SS BOND : angle 0.20479 ( 16) covalent geometry : bond 0.00256 (24688) covalent geometry : angle 0.49208 (33504) ********************** 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 309 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 2.495 Fit side-chains REVERT: A 88 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7799 (t0) REVERT: A 259 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7990 (tttm) REVERT: A 281 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7415 (mtm110) REVERT: B 88 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7800 (t0) REVERT: B 259 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7998 (tttm) REVERT: B 281 ARG cc_start: 0.7698 (ttp-170) cc_final: 0.7427 (mtm110) REVERT: C 88 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7805 (t0) REVERT: C 259 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8003 (tttm) REVERT: C 281 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.7377 (mtt90) REVERT: D 88 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7812 (t0) REVERT: D 259 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7998 (tttm) REVERT: D 281 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7426 (mtm110) REVERT: E 278 GLU cc_start: 0.7664 (tt0) cc_final: 0.7458 (tt0) REVERT: G 54 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8182 (tt) REVERT: G 278 GLU cc_start: 0.7776 (tt0) cc_final: 0.7352 (mp0) REVERT: G 284 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8181 (mtpp) REVERT: G 327 ASP cc_start: 0.8147 (m-30) cc_final: 0.7945 (m-30) REVERT: H 54 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8165 (tt) outliers start: 34 outliers final: 20 residues processed: 295 average time/residue: 1.6255 time to fit residues: 537.8916 Evaluate side-chains 299 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 6 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 309 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 326 GLN C 326 GLN D 326 GLN 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 = 0.123057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.097338 restraints weight = 20387.517| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.43 r_work: 0.3168 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24728 Z= 0.213 Angle : 0.598 12.190 33520 Z= 0.317 Chirality : 0.050 0.233 3712 Planarity : 0.005 0.052 4440 Dihedral : 7.570 55.491 3712 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.88 % Allowed : 16.14 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3136 helix: 1.44 (0.15), residues: 1288 sheet: 0.69 (0.30), residues: 296 loop : -1.10 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 289 HIS 0.008 0.001 HIS G 251 PHE 0.012 0.002 PHE B 229 TYR 0.017 0.002 TYR A 333 ARG 0.008 0.001 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.06091 ( 1016) hydrogen bonds : angle 4.21560 ( 2832) metal coordination : bond 0.00469 ( 32) SS BOND : bond 0.00165 ( 8) SS BOND : angle 0.32259 ( 16) covalent geometry : bond 0.00511 (24688) covalent geometry : angle 0.59844 (33504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18056.98 seconds wall clock time: 310 minutes 58.20 seconds (18658.20 seconds total)