Starting phenix.real_space_refine on Sun Jan 26 02:33:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yak_39101/01_2025/8yak_39101_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yak_39101/01_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_39101/01_2025/8yak_39101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yak_39101/01_2025/8yak_39101.map" model { file = "/net/cci-nas-00/data/ceres_data/8yak_39101/01_2025/8yak_39101_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yak_39101/01_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-5571/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: 13.53, per 1000 atoms: 0.56 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: 6.37 Conformation dependent library (CDL) restraints added in 2.9 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: 2.94 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: 8.36 Time building geometry restraints manager: 6.90 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: 0.20 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: 1.790 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: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 55.590 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.120 ------------------------------------------------------------------------------- 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 : 0.006 0.133 24688 Z= 0.367 Angle : 0.678 13.641 33504 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 *********************** 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 : 2.672 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: 1.7545 time to fit residues: 941.2335 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 : 2.822 ------------------------------------------------------------------------------- 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: 4.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.122636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096810 restraints weight = 22530.834| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.40 r_work: 0.3161 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24688 Z= 0.329 Angle : 0.606 5.233 33504 Z= 0.325 Chirality : 0.050 0.243 3712 Planarity : 0.005 0.048 4440 Dihedral : 8.288 69.042 3720 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.45 % Allowed : 14.83 % Favored : 82.72 % 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: 0.24 (0.15), residues: 3136 helix: 1.38 (0.15), residues: 1288 sheet: 0.62 (0.30), residues: 296 loop : -1.01 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 289 HIS 0.009 0.002 HIS F 251 PHE 0.014 0.002 PHE A 229 TYR 0.017 0.002 TYR B 333 ARG 0.006 0.001 ARG B 34 *********************** 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 : 2.766 Fit side-chains REVERT: A 88 ASP cc_start: 0.8266 (p0) cc_final: 0.7855 (t0) REVERT: A 259 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8087 (tttm) REVERT: A 281 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7347 (mtt90) REVERT: B 88 ASP cc_start: 0.8258 (p0) cc_final: 0.7863 (t0) REVERT: B 259 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8090 (tttm) REVERT: B 281 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7351 (mtt90) REVERT: C 88 ASP cc_start: 0.8280 (p0) cc_final: 0.7867 (t0) REVERT: C 259 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8088 (tttm) REVERT: C 281 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7395 (mtt90) REVERT: D 88 ASP cc_start: 0.8288 (p0) cc_final: 0.7875 (t0) REVERT: D 259 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8089 (tttm) REVERT: D 281 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7401 (mtt90) REVERT: E 278 GLU cc_start: 0.7821 (tt0) cc_final: 0.7479 (mp0) REVERT: G 278 GLU cc_start: 0.7817 (tt0) cc_final: 0.7472 (mp0) REVERT: G 284 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8172 (mtpp) REVERT: G 327 ASP cc_start: 0.8099 (m-30) cc_final: 0.7830 (m-30) REVERT: H 284 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8164 (mtpp) REVERT: H 327 ASP cc_start: 0.8093 (m-30) cc_final: 0.7826 (m-30) outliers start: 60 outliers final: 26 residues processed: 342 average time/residue: 1.6916 time to fit residues: 650.7249 Evaluate side-chains 295 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 2.538 ------------------------------------------------------------------------------- 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: 0.9990 chunk 137 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 230 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.123366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097665 restraints weight = 22279.887| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.44 r_work: 0.3164 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24688 Z= 0.289 Angle : 0.565 5.097 33504 Z= 0.304 Chirality : 0.049 0.233 3712 Planarity : 0.005 0.047 4440 Dihedral : 7.882 61.865 3712 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.45 % Allowed : 14.58 % Favored : 82.97 % 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: 1.37 (0.15), residues: 1288 sheet: 0.69 (0.31), residues: 296 loop : -1.05 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.008 0.001 HIS C 271 PHE 0.012 0.002 PHE C 229 TYR 0.016 0.002 TYR C 333 ARG 0.004 0.001 ARG A 34 *********************** 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 341 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 2.790 Fit side-chains REVERT: A 88 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7848 (t0) REVERT: A 259 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8049 (tttm) REVERT: A 281 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7357 (mtt90) REVERT: B 88 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7856 (t0) REVERT: B 259 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8045 (tttm) REVERT: B 281 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7352 (mtt90) REVERT: C 88 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7858 (t0) REVERT: C 259 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8054 (tttm) REVERT: C 281 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7348 (mtt90) REVERT: D 88 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7847 (t0) REVERT: D 259 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8043 (tttm) REVERT: D 281 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7346 (mtt90) REVERT: E 278 GLU cc_start: 0.7842 (tt0) cc_final: 0.7375 (mp0) REVERT: G 278 GLU cc_start: 0.7832 (tt0) cc_final: 0.7397 (mp0) REVERT: G 284 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8175 (mtpp) REVERT: G 327 ASP cc_start: 0.8182 (m-30) cc_final: 0.7948 (m-30) REVERT: H 284 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8171 (mtpp) REVERT: H 327 ASP cc_start: 0.8184 (m-30) cc_final: 0.7951 (m-30) outliers start: 60 outliers final: 32 residues processed: 306 average time/residue: 1.7697 time to fit residues: 606.8915 Evaluate side-chains 316 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 2.797 ------------------------------------------------------------------------------- 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 325 ILE 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 325 ILE 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 325 ILE 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 325 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 105 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.124484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098856 restraints weight = 21764.070| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.47 r_work: 0.3190 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 24688 Z= 0.234 Angle : 0.528 5.201 33504 Z= 0.282 Chirality : 0.047 0.226 3712 Planarity : 0.005 0.038 4440 Dihedral : 7.217 53.092 3712 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.17 % Allowed : 14.79 % Favored : 83.05 % 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: 0.29 (0.15), residues: 3136 helix: 1.49 (0.15), residues: 1288 sheet: 0.70 (0.30), residues: 296 loop : -1.06 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 289 HIS 0.007 0.001 HIS F 251 PHE 0.011 0.001 PHE D 229 TYR 0.015 0.002 TYR C 333 ARG 0.003 0.000 ARG F 50 *********************** 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 336 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 2.821 Fit side-chains REVERT: A 88 ASP cc_start: 0.8308 (p0) cc_final: 0.7841 (t0) REVERT: A 259 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8025 (tttm) REVERT: A 281 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7361 (mtt90) REVERT: B 88 ASP cc_start: 0.8305 (p0) cc_final: 0.7843 (t0) REVERT: B 259 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8031 (tttm) REVERT: B 281 ARG cc_start: 0.7702 (ttp-170) cc_final: 0.7349 (mtt90) REVERT: C 88 ASP cc_start: 0.8288 (p0) cc_final: 0.7843 (t0) REVERT: C 259 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8003 (tttm) REVERT: C 281 ARG cc_start: 0.7712 (ttp-170) cc_final: 0.7360 (mtt90) REVERT: D 88 ASP cc_start: 0.8290 (p0) cc_final: 0.7847 (t0) REVERT: D 259 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8009 (tttm) REVERT: D 281 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7367 (mtt90) REVERT: E 278 GLU cc_start: 0.7817 (tt0) cc_final: 0.7367 (mp0) REVERT: G 278 GLU cc_start: 0.7771 (tt0) cc_final: 0.7364 (mp0) REVERT: G 284 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8173 (mtpp) REVERT: G 327 ASP cc_start: 0.8127 (m-30) cc_final: 0.7893 (m-30) REVERT: H 327 ASP cc_start: 0.8137 (m-30) cc_final: 0.7905 (m-30) outliers start: 53 outliers final: 27 residues processed: 313 average time/residue: 1.7847 time to fit residues: 630.3135 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 : 2.636 ------------------------------------------------------------------------------- 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 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 30 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: 9.9990 chunk 54 optimal weight: 8.9990 chunk 249 optimal weight: 1.9990 chunk 193 optimal weight: 0.0970 chunk 162 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102689 restraints weight = 21696.031| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.48 r_work: 0.3244 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 24688 Z= 0.123 Angle : 0.450 5.531 33504 Z= 0.236 Chirality : 0.044 0.223 3712 Planarity : 0.004 0.033 4440 Dihedral : 5.931 51.467 3712 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.35 % Allowed : 15.44 % 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: 0.56 (0.15), residues: 3136 helix: 1.76 (0.15), residues: 1288 sheet: 0.76 (0.29), residues: 296 loop : -0.93 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 289 HIS 0.007 0.001 HIS E 251 PHE 0.006 0.001 PHE C 229 TYR 0.011 0.001 TYR C 333 ARG 0.003 0.000 ARG E 50 *********************** 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 320 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 2.786 Fit side-chains REVERT: A 88 ASP cc_start: 0.8309 (p0) cc_final: 0.7803 (t0) REVERT: A 259 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7991 (tttm) REVERT: A 281 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.7372 (mtt90) REVERT: B 88 ASP cc_start: 0.8296 (p0) cc_final: 0.7800 (t0) REVERT: B 259 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7998 (tttm) REVERT: B 281 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7362 (mtt90) REVERT: C 88 ASP cc_start: 0.8309 (p0) cc_final: 0.7820 (t0) REVERT: C 259 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8208 (ttpp) REVERT: C 281 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7343 (mtt90) REVERT: D 88 ASP cc_start: 0.8312 (p0) cc_final: 0.7829 (t0) REVERT: D 259 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8221 (ttpp) REVERT: D 281 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7379 (mtt90) REVERT: E 278 GLU cc_start: 0.7683 (tt0) cc_final: 0.7313 (mp0) REVERT: G 278 GLU cc_start: 0.7700 (tt0) cc_final: 0.7298 (mp0) REVERT: G 327 ASP cc_start: 0.8116 (m-30) cc_final: 0.7906 (m-30) REVERT: H 327 ASP cc_start: 0.8143 (m-30) cc_final: 0.7937 (m-30) outliers start: 33 outliers final: 24 residues processed: 306 average time/residue: 1.7225 time to fit residues: 592.4850 Evaluate side-chains 310 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 2.856 ------------------------------------------------------------------------------- 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 345 MET Chi-restraints excluded: chain A residue 416 ASP 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 345 MET Chi-restraints excluded: chain B residue 416 ASP 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 416 ASP 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 416 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 228 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 256 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 chunk 295 optimal weight: 20.0000 chunk 188 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.123627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098126 restraints weight = 20621.512| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.43 r_work: 0.3159 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24688 Z= 0.308 Angle : 0.569 6.873 33504 Z= 0.304 Chirality : 0.049 0.230 3712 Planarity : 0.005 0.048 4440 Dihedral : 7.447 55.237 3712 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.37 % Allowed : 14.50 % 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: 0.33 (0.15), residues: 3136 helix: 1.51 (0.15), residues: 1288 sheet: 0.79 (0.30), residues: 296 loop : -1.04 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 289 HIS 0.008 0.001 HIS E 251 PHE 0.011 0.002 PHE D 229 TYR 0.017 0.002 TYR A 333 ARG 0.003 0.001 ARG F 50 *********************** 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 331 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 2.843 Fit side-chains REVERT: A 88 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7803 (t0) REVERT: A 259 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8032 (tttm) REVERT: A 281 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.7363 (mtt90) REVERT: B 88 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7807 (t0) REVERT: B 259 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8052 (tttm) REVERT: B 281 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7359 (mtt90) REVERT: C 88 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7829 (t0) REVERT: C 259 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7992 (tttm) REVERT: C 281 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7370 (mtt90) REVERT: D 88 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7858 (t0) REVERT: D 259 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8001 (tttm) REVERT: D 281 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7370 (mtt90) REVERT: E 278 GLU cc_start: 0.7812 (tt0) cc_final: 0.7372 (mp0) REVERT: G 278 GLU cc_start: 0.7767 (tt0) cc_final: 0.7335 (mp0) REVERT: G 327 ASP cc_start: 0.8117 (m-30) cc_final: 0.7884 (m-30) REVERT: H 327 ASP cc_start: 0.8126 (m-30) cc_final: 0.7893 (m-30) outliers start: 58 outliers final: 24 residues processed: 299 average time/residue: 1.7882 time to fit residues: 600.2049 Evaluate side-chains 298 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 2.966 ------------------------------------------------------------------------------- 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 325 ILE 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 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 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: 2.9990 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: 0.9980 chunk 137 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.123779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098282 restraints weight = 20497.324| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.42 r_work: 0.3177 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24688 Z= 0.294 Angle : 0.564 7.570 33504 Z= 0.301 Chirality : 0.049 0.230 3712 Planarity : 0.005 0.048 4440 Dihedral : 7.428 54.322 3712 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.21 % Allowed : 14.83 % Favored : 82.97 % 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: 0.24 (0.14), residues: 3136 helix: 1.45 (0.15), residues: 1288 sheet: 0.74 (0.30), residues: 296 loop : -1.10 (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 0.011 0.002 PHE A 229 TYR 0.017 0.002 TYR C 333 ARG 0.004 0.000 ARG H 50 *********************** 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 321 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 2.554 Fit side-chains REVERT: A 88 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7837 (t0) REVERT: A 259 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8053 (tttm) REVERT: A 281 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7411 (mtt90) REVERT: B 88 ASP cc_start: 0.8305 (p0) cc_final: 0.7832 (t0) REVERT: B 259 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8063 (tttm) REVERT: B 281 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7395 (mtt90) REVERT: C 88 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7850 (t0) REVERT: C 259 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8010 (tttm) REVERT: C 281 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7410 (mtt90) REVERT: D 88 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7871 (t0) REVERT: D 259 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8007 (tttm) REVERT: D 281 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7404 (mtt90) REVERT: E 278 GLU cc_start: 0.7858 (tt0) cc_final: 0.7471 (mp0) REVERT: G 278 GLU cc_start: 0.7826 (tt0) cc_final: 0.7433 (mp0) REVERT: G 327 ASP cc_start: 0.8127 (m-30) cc_final: 0.7902 (m-30) REVERT: H 327 ASP cc_start: 0.8136 (m-30) cc_final: 0.7912 (m-30) outliers start: 54 outliers final: 26 residues processed: 299 average time/residue: 1.7983 time to fit residues: 602.8358 Evaluate side-chains 295 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 2.749 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 233 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098757 restraints weight = 20479.894| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.42 r_work: 0.3184 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24688 Z= 0.263 Angle : 0.547 8.257 33504 Z= 0.291 Chirality : 0.048 0.229 3712 Planarity : 0.005 0.042 4440 Dihedral : 7.264 53.474 3712 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.84 % Allowed : 15.73 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.14), residues: 3136 helix: 1.49 (0.15), residues: 1288 sheet: 0.73 (0.30), residues: 296 loop : -1.09 (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 H 251 PHE 0.010 0.002 PHE C 229 TYR 0.016 0.002 TYR C 333 ARG 0.004 0.000 ARG F 50 *********************** 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 309 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 2.561 Fit side-chains REVERT: A 88 ASP cc_start: 0.8298 (p0) cc_final: 0.7814 (t0) REVERT: A 259 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8038 (tttm) REVERT: A 281 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7370 (mtt90) REVERT: B 88 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7818 (t0) REVERT: B 259 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8048 (tttm) REVERT: B 281 ARG cc_start: 0.7692 (ttp-170) cc_final: 0.7367 (mtt90) REVERT: C 88 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7839 (t0) REVERT: C 259 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8016 (tttm) REVERT: C 281 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.7385 (mtt90) REVERT: D 88 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7867 (t0) REVERT: D 259 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8012 (tttm) REVERT: D 281 ARG cc_start: 0.7702 (ttp-170) cc_final: 0.7375 (mtt90) REVERT: E 278 GLU cc_start: 0.7839 (tt0) cc_final: 0.7426 (mp0) REVERT: G 278 GLU cc_start: 0.7808 (tt0) cc_final: 0.7399 (mp0) REVERT: G 327 ASP cc_start: 0.8119 (m-30) cc_final: 0.7890 (m-30) REVERT: H 327 ASP cc_start: 0.8139 (m-30) cc_final: 0.7910 (m-30) outliers start: 45 outliers final: 29 residues processed: 284 average time/residue: 1.8649 time to fit residues: 592.3267 Evaluate side-chains 305 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 123 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 287 optimal weight: 0.0980 chunk 101 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 201 optimal weight: 0.4980 chunk 58 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.126988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101406 restraints weight = 21419.538| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.48 r_work: 0.3231 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 24688 Z= 0.137 Angle : 0.468 8.135 33504 Z= 0.244 Chirality : 0.044 0.224 3712 Planarity : 0.004 0.037 4440 Dihedral : 6.131 51.266 3712 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.35 % Allowed : 16.22 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.15), residues: 3136 helix: 1.72 (0.15), residues: 1288 sheet: 0.75 (0.29), residues: 296 loop : -0.98 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 289 HIS 0.007 0.001 HIS E 251 PHE 0.006 0.001 PHE C 229 TYR 0.012 0.001 TYR C 333 ARG 0.004 0.000 ARG F 50 *********************** 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 312 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 2.431 Fit side-chains REVERT: A 88 ASP cc_start: 0.8311 (p0) cc_final: 0.7798 (t0) REVERT: A 259 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8030 (tttm) REVERT: A 281 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7420 (mtt90) REVERT: B 88 ASP cc_start: 0.8304 (p0) cc_final: 0.7794 (t0) REVERT: B 259 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8029 (tttm) REVERT: B 281 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7417 (mtt90) REVERT: C 88 ASP cc_start: 0.8329 (p0) cc_final: 0.7828 (t0) REVERT: C 259 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7998 (tttm) REVERT: C 281 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7409 (mtt90) REVERT: D 88 ASP cc_start: 0.8338 (p0) cc_final: 0.7847 (t0) REVERT: D 259 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8003 (tttm) REVERT: D 281 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7465 (mtm110) REVERT: E 278 GLU cc_start: 0.7777 (tt0) cc_final: 0.7374 (mp0) REVERT: G 278 GLU cc_start: 0.7752 (tt0) cc_final: 0.7356 (mp0) REVERT: G 327 ASP cc_start: 0.8137 (m-30) cc_final: 0.7935 (m-30) REVERT: H 327 ASP cc_start: 0.8157 (m-30) cc_final: 0.7956 (m-30) outliers start: 33 outliers final: 20 residues processed: 296 average time/residue: 1.8674 time to fit residues: 616.3609 Evaluate side-chains 299 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 275 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 221 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 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 = 0.3523 r_free = 0.3523 target = 0.122651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096921 restraints weight = 20439.615| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.43 r_work: 0.3161 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 24688 Z= 0.371 Angle : 0.616 11.568 33504 Z= 0.328 Chirality : 0.051 0.233 3712 Planarity : 0.005 0.058 4440 Dihedral : 7.733 55.725 3712 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.72 % Allowed : 15.73 % Favored : 82.56 % 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: 0.20 (0.14), residues: 3136 helix: 1.39 (0.15), residues: 1288 sheet: 0.62 (0.28), residues: 336 loop : -1.11 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 289 HIS 0.008 0.001 HIS G 251 PHE 0.013 0.002 PHE A 229 TYR 0.018 0.002 TYR C 333 ARG 0.009 0.001 ARG A 34 ********************** 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 306 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 2.810 Fit side-chains REVERT: A 88 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7843 (t0) REVERT: A 259 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8061 (tttm) REVERT: A 281 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7409 (mtt90) REVERT: B 88 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7840 (t0) REVERT: B 259 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8076 (tttm) REVERT: B 281 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.7395 (mtt90) REVERT: C 88 ASP cc_start: 0.8329 (p0) cc_final: 0.7860 (t0) REVERT: C 259 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8019 (tttm) REVERT: C 281 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7414 (mtt90) REVERT: D 88 ASP cc_start: 0.8319 (p0) cc_final: 0.7864 (t0) REVERT: D 259 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8018 (tttm) REVERT: D 281 ARG cc_start: 0.7746 (ttp-170) cc_final: 0.7416 (mtt90) REVERT: E 278 GLU cc_start: 0.7867 (tt0) cc_final: 0.7416 (mp0) REVERT: G 278 GLU cc_start: 0.7832 (tt0) cc_final: 0.7428 (mp0) REVERT: G 327 ASP cc_start: 0.8141 (m-30) cc_final: 0.7912 (m-30) REVERT: H 327 ASP cc_start: 0.8147 (m-30) cc_final: 0.7918 (m-30) outliers start: 42 outliers final: 20 residues processed: 284 average time/residue: 1.8539 time to fit residues: 587.7560 Evaluate side-chains 284 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 2.538 ------------------------------------------------------------------------------- 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 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 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 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 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 6 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 309 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.125236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099786 restraints weight = 20842.531| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.44 r_work: 0.3199 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24688 Z= 0.201 Angle : 0.520 10.706 33504 Z= 0.274 Chirality : 0.046 0.226 3712 Planarity : 0.004 0.038 4440 Dihedral : 6.884 52.068 3712 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.39 % Allowed : 16.38 % Favored : 82.23 % 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: 0.35 (0.15), residues: 3136 helix: 1.57 (0.15), residues: 1288 sheet: 0.74 (0.30), residues: 296 loop : -1.06 (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 0.008 0.001 PHE A 229 TYR 0.014 0.001 TYR C 333 ARG 0.008 0.000 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17671.15 seconds wall clock time: 317 minutes 12.39 seconds (19032.39 seconds total)