Starting phenix.real_space_refine on Fri Sep 19 07:36:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yak_39101/09_2025/8yak_39101_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yak_39101/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yak_39101/09_2025/8yak_39101_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yak_39101/09_2025/8yak_39101_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yak_39101/09_2025/8yak_39101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yak_39101/09_2025/8yak_39101.map" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.25, per 1000 atoms: 0.22 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: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.88 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: 4.59 Time building geometry restraints manager: 2.46 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.690 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.356 24728 Z= 0.362 Angle : 0.678 13.641 33520 Z= 0.332 Chirality : 0.046 0.315 3712 Planarity : 0.003 0.024 4440 Dihedral : 17.341 87.246 9048 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.51 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (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 ARG 0.002 0.000 ARG F 281 TYR 0.010 0.001 TYR A 333 PHE 0.008 0.001 PHE H 229 TRP 0.007 0.001 TRP F 289 HIS 0.007 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00563 (24688) covalent geometry : angle 0.67815 (33504) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.38906 ( 16) hydrogen bonds : bond 0.16984 ( 1016) hydrogen bonds : angle 6.30089 ( 2832) metal coordination : bond 0.17767 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 479 time to evaluate : 0.954 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: 0.7579 time to fit residues: 406.4974 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 : 0.843 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.6980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 271 HIS A 326 GLN A 344 ASN B 26 HIS B 271 HIS B 326 GLN B 344 ASN C 26 HIS C 271 HIS C 326 GLN C 344 ASN D 26 HIS D 271 HIS D 326 GLN D 344 ASN 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098671 restraints weight = 23138.584| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.41 r_work: 0.3188 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.796 24728 Z= 0.491 Angle : 0.551 5.083 33520 Z= 0.294 Chirality : 0.048 0.243 3712 Planarity : 0.005 0.037 4440 Dihedral : 7.815 62.584 3720 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.49 % Allowed : 14.91 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.15), residues: 3136 helix: 1.48 (0.15), residues: 1296 sheet: 0.66 (0.30), residues: 296 loop : -0.93 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 34 TYR 0.016 0.002 TYR B 333 PHE 0.012 0.002 PHE B 229 TRP 0.008 0.001 TRP F 289 HIS 0.009 0.002 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00368 (24688) covalent geometry : angle 0.55140 (33504) SS BOND : bond 0.00202 ( 8) SS BOND : angle 0.48531 ( 16) hydrogen bonds : bond 0.05525 ( 1016) hydrogen bonds : angle 4.32126 ( 2832) metal coordination : bond 0.38730 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 314 time to evaluate : 0.808 Fit side-chains REVERT: A 88 ASP cc_start: 0.8197 (p0) cc_final: 0.7795 (t0) REVERT: A 259 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8061 (tttm) REVERT: A 281 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7366 (mtt90) REVERT: B 88 ASP cc_start: 0.8198 (p0) cc_final: 0.7805 (t0) REVERT: B 259 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8062 (tttm) REVERT: B 281 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.7366 (mtt90) REVERT: C 88 ASP cc_start: 0.8230 (p0) cc_final: 0.7828 (t0) REVERT: C 259 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8054 (tttm) REVERT: C 281 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7378 (mtt90) REVERT: D 88 ASP cc_start: 0.8242 (p0) cc_final: 0.7840 (t0) REVERT: D 259 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8060 (tttm) REVERT: D 281 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7379 (mtt90) REVERT: E 88 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: E 278 GLU cc_start: 0.7796 (tt0) cc_final: 0.7516 (mp0) REVERT: F 88 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: G 88 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: G 278 GLU cc_start: 0.7763 (tt0) cc_final: 0.7476 (mp0) REVERT: G 284 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8176 (mtpp) REVERT: G 327 ASP cc_start: 0.8080 (m-30) cc_final: 0.7817 (m-30) REVERT: H 88 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: H 284 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8166 (mtpp) REVERT: H 327 ASP cc_start: 0.8080 (m-30) cc_final: 0.7819 (m-30) outliers start: 61 outliers final: 25 residues processed: 348 average time/residue: 0.7709 time to fit residues: 300.4533 Evaluate side-chains 318 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 289 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 52 ASP 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 52 ASP 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 162 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 171 optimal weight: 0.0870 overall best weight: 3.6164 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.123396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097709 restraints weight = 22059.381| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.48 r_work: 0.3168 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24728 Z= 0.196 Angle : 0.582 5.365 33520 Z= 0.313 Chirality : 0.050 0.232 3712 Planarity : 0.005 0.050 4440 Dihedral : 7.841 58.952 3712 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.17 % Allowed : 15.03 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3136 helix: 1.40 (0.15), residues: 1288 sheet: 0.65 (0.30), residues: 296 loop : -1.02 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 50 TYR 0.017 0.002 TYR A 333 PHE 0.013 0.002 PHE A 229 TRP 0.007 0.001 TRP G 289 HIS 0.009 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00469 (24688) covalent geometry : angle 0.58195 (33504) SS BOND : bond 0.00229 ( 8) SS BOND : angle 0.38305 ( 16) hydrogen bonds : bond 0.06112 ( 1016) hydrogen bonds : angle 4.33365 ( 2832) metal coordination : bond 0.00589 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 0.689 Fit side-chains REVERT: A 88 ASP cc_start: 0.8280 (p0) cc_final: 0.7843 (t0) REVERT: A 259 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8042 (tttm) REVERT: A 281 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7350 (mtt90) REVERT: B 88 ASP cc_start: 0.8266 (p0) cc_final: 0.7855 (t0) REVERT: B 259 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8048 (tttm) REVERT: B 281 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7362 (mtt90) REVERT: C 88 ASP cc_start: 0.8287 (p0) cc_final: 0.7853 (t0) REVERT: C 259 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8059 (tttm) REVERT: C 281 ARG cc_start: 0.7712 (ttp-170) cc_final: 0.7335 (mtt90) REVERT: D 88 ASP cc_start: 0.8290 (p0) cc_final: 0.7853 (t0) REVERT: D 259 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8029 (tttm) REVERT: D 281 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7355 (mtt90) REVERT: E 278 GLU cc_start: 0.7840 (tt0) cc_final: 0.7381 (mp0) REVERT: G 278 GLU cc_start: 0.7845 (tt0) cc_final: 0.7411 (mp0) REVERT: G 327 ASP cc_start: 0.8119 (m-30) cc_final: 0.7877 (m-30) REVERT: H 327 ASP cc_start: 0.8113 (m-30) cc_final: 0.7871 (m-30) outliers start: 53 outliers final: 26 residues processed: 308 average time/residue: 0.7564 time to fit residues: 260.9124 Evaluate side-chains 304 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 392 THR 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 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 208 optimal weight: 7.9990 chunk 210 optimal weight: 0.0370 chunk 29 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 212 optimal weight: 0.4980 chunk 63 optimal weight: 10.0000 overall best weight: 3.1064 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.123928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098315 restraints weight = 21512.728| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.46 r_work: 0.3181 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 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 0.029 24728 Z= 0.173 Angle : 0.550 5.133 33520 Z= 0.295 Chirality : 0.048 0.230 3712 Planarity : 0.005 0.044 4440 Dihedral : 7.370 52.712 3712 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.41 % Allowed : 14.71 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3136 helix: 1.43 (0.15), residues: 1288 sheet: 0.71 (0.30), residues: 296 loop : -1.06 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 50 TYR 0.016 0.002 TYR D 333 PHE 0.011 0.002 PHE B 229 TRP 0.007 0.001 TRP F 289 HIS 0.008 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00408 (24688) covalent geometry : angle 0.54986 (33504) SS BOND : bond 0.00175 ( 8) SS BOND : angle 0.25498 ( 16) hydrogen bonds : bond 0.05546 ( 1016) hydrogen bonds : angle 4.18857 ( 2832) metal coordination : bond 0.00359 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 280 time to evaluate : 0.959 Fit side-chains REVERT: A 88 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7833 (t0) REVERT: A 259 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8012 (tttm) REVERT: A 281 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7364 (mtt90) REVERT: B 88 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7856 (t0) REVERT: B 259 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8006 (tttm) REVERT: B 281 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7350 (mtt90) REVERT: C 88 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7874 (t0) REVERT: C 259 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8035 (tttm) REVERT: C 281 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7356 (mtt90) REVERT: D 88 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7849 (t0) REVERT: D 259 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8005 (tttm) REVERT: D 281 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7361 (mtt90) REVERT: E 278 GLU cc_start: 0.7849 (tt0) cc_final: 0.7429 (mp0) REVERT: G 278 GLU cc_start: 0.7809 (tt0) cc_final: 0.7370 (mp0) REVERT: G 327 ASP cc_start: 0.8138 (m-30) cc_final: 0.7908 (m-30) REVERT: H 327 ASP cc_start: 0.8135 (m-30) cc_final: 0.7905 (m-30) outliers start: 59 outliers final: 29 residues processed: 310 average time/residue: 0.7777 time to fit residues: 269.4488 Evaluate side-chains 305 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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 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 392 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 305 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN C 326 GLN D 326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096915 restraints weight = 21144.138| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.44 r_work: 0.3153 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 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 : 0.006 0.043 24728 Z= 0.241 Angle : 0.619 6.302 33520 Z= 0.334 Chirality : 0.051 0.236 3712 Planarity : 0.006 0.057 4440 Dihedral : 8.014 57.909 3712 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.70 % Allowed : 14.83 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.14), residues: 3136 helix: 1.25 (0.15), residues: 1288 sheet: 0.57 (0.28), residues: 336 loop : -1.17 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 50 TYR 0.018 0.002 TYR D 333 PHE 0.013 0.002 PHE F 229 TRP 0.008 0.002 TRP H 289 HIS 0.008 0.002 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00583 (24688) covalent geometry : angle 0.61890 (33504) SS BOND : bond 0.00222 ( 8) SS BOND : angle 0.32890 ( 16) hydrogen bonds : bond 0.06653 ( 1016) hydrogen bonds : angle 4.34668 ( 2832) metal coordination : bond 0.00513 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.896 Fit side-chains REVERT: A 88 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7852 (t0) REVERT: A 259 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8041 (tttm) REVERT: A 281 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.7461 (mtm110) REVERT: A 327 ASP cc_start: 0.7974 (m-30) cc_final: 0.7678 (m-30) REVERT: B 88 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7858 (t0) REVERT: B 259 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8028 (tttm) REVERT: B 281 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7466 (mtm110) REVERT: B 327 ASP cc_start: 0.7980 (m-30) cc_final: 0.7694 (m-30) REVERT: C 88 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7867 (t0) REVERT: C 259 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8058 (tttm) REVERT: C 281 ARG cc_start: 0.7725 (ttp-170) cc_final: 0.7461 (mtm110) REVERT: C 327 ASP cc_start: 0.7966 (m-30) cc_final: 0.7680 (m-30) REVERT: D 88 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7875 (t0) REVERT: D 259 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8048 (tttm) REVERT: D 281 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7468 (mtm110) REVERT: D 327 ASP cc_start: 0.7973 (m-30) cc_final: 0.7689 (m-30) REVERT: E 278 GLU cc_start: 0.7846 (tt0) cc_final: 0.7370 (mp0) REVERT: G 278 GLU cc_start: 0.7822 (tt0) cc_final: 0.7372 (mp0) REVERT: G 327 ASP cc_start: 0.8095 (m-30) cc_final: 0.7862 (m-30) REVERT: H 327 ASP cc_start: 0.8108 (m-30) cc_final: 0.7875 (m-30) outliers start: 66 outliers final: 28 residues processed: 302 average time/residue: 0.7761 time to fit residues: 262.1841 Evaluate side-chains 293 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 325 ILE 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 325 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 154 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.123844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098141 restraints weight = 20934.348| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.45 r_work: 0.3180 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 24728 Z= 0.160 Angle : 0.537 6.125 33520 Z= 0.287 Chirality : 0.047 0.228 3712 Planarity : 0.005 0.040 4440 Dihedral : 7.330 52.821 3712 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.33 % Allowed : 14.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.15), residues: 3136 helix: 1.43 (0.15), residues: 1288 sheet: 0.69 (0.30), residues: 296 loop : -1.12 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 50 TYR 0.016 0.002 TYR B 333 PHE 0.010 0.002 PHE B 229 TRP 0.006 0.001 TRP F 289 HIS 0.007 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00376 (24688) covalent geometry : angle 0.53666 (33504) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.21460 ( 16) hydrogen bonds : bond 0.05318 ( 1016) hydrogen bonds : angle 4.13124 ( 2832) metal coordination : bond 0.00323 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 264 time to evaluate : 0.884 Fit side-chains REVERT: A 88 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7848 (t0) REVERT: A 259 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8018 (tttm) REVERT: A 281 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7386 (mtt90) REVERT: B 88 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7856 (t0) REVERT: B 259 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8025 (tttm) REVERT: B 281 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7373 (mtt90) REVERT: C 88 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7873 (t0) REVERT: C 259 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8047 (tttm) REVERT: C 281 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7380 (mtt90) REVERT: D 88 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7875 (t0) REVERT: D 259 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8031 (tttm) REVERT: D 281 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7391 (mtt90) REVERT: E 278 GLU cc_start: 0.7846 (tt0) cc_final: 0.7442 (mp0) REVERT: G 278 GLU cc_start: 0.7816 (tt0) cc_final: 0.7402 (mp0) REVERT: G 327 ASP cc_start: 0.8131 (m-30) cc_final: 0.7899 (m-30) REVERT: H 327 ASP cc_start: 0.8137 (m-30) cc_final: 0.7906 (m-30) outliers start: 57 outliers final: 27 residues processed: 296 average time/residue: 0.7799 time to fit residues: 257.4012 Evaluate side-chains 309 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 208 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.123490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097761 restraints weight = 20796.697| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.45 r_work: 0.3173 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24728 Z= 0.175 Angle : 0.555 7.595 33520 Z= 0.297 Chirality : 0.048 0.229 3712 Planarity : 0.005 0.043 4440 Dihedral : 7.381 53.979 3712 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.04 % Allowed : 15.65 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 3136 helix: 1.40 (0.15), residues: 1288 sheet: 0.67 (0.30), residues: 296 loop : -1.12 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 50 TYR 0.016 0.002 TYR C 333 PHE 0.011 0.002 PHE B 229 TRP 0.006 0.001 TRP G 289 HIS 0.007 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00416 (24688) covalent geometry : angle 0.55488 (33504) SS BOND : bond 0.00153 ( 8) SS BOND : angle 0.23800 ( 16) hydrogen bonds : bond 0.05624 ( 1016) hydrogen bonds : angle 4.16265 ( 2832) metal coordination : bond 0.00365 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.987 Fit side-chains REVERT: A 88 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7840 (t0) REVERT: A 259 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8002 (tttm) REVERT: A 281 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7380 (mtt90) REVERT: B 88 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7837 (t0) REVERT: B 259 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8019 (tttm) REVERT: B 281 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7380 (mtt90) REVERT: C 88 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7861 (t0) REVERT: C 259 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8041 (tttm) REVERT: C 281 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7380 (mtt90) REVERT: D 88 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7865 (t0) REVERT: D 259 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8018 (tttm) REVERT: D 281 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7386 (mtt90) REVERT: E 278 GLU cc_start: 0.7850 (tt0) cc_final: 0.7423 (mp0) REVERT: G 278 GLU cc_start: 0.7837 (tt0) cc_final: 0.7439 (mp0) REVERT: G 327 ASP cc_start: 0.8127 (m-30) cc_final: 0.7897 (m-30) REVERT: H 327 ASP cc_start: 0.8127 (m-30) cc_final: 0.7899 (m-30) outliers start: 50 outliers final: 37 residues processed: 288 average time/residue: 0.8019 time to fit residues: 258.3465 Evaluate side-chains 315 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 270 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 362 GLU 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 362 GLU 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 362 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 325 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 362 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.125185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099651 restraints weight = 20758.711| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.44 r_work: 0.3197 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24728 Z= 0.133 Angle : 0.509 7.769 33520 Z= 0.270 Chirality : 0.046 0.226 3712 Planarity : 0.004 0.040 4440 Dihedral : 6.855 52.468 3712 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.96 % Allowed : 15.89 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 3136 helix: 1.52 (0.15), residues: 1288 sheet: 0.72 (0.30), residues: 296 loop : -1.08 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 50 TYR 0.014 0.001 TYR C 333 PHE 0.009 0.001 PHE B 229 TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00306 (24688) covalent geometry : angle 0.50941 (33504) SS BOND : bond 0.00124 ( 8) SS BOND : angle 0.19796 ( 16) hydrogen bonds : bond 0.04743 ( 1016) hydrogen bonds : angle 4.02568 ( 2832) metal coordination : bond 0.00283 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 0.953 Fit side-chains REVERT: A 88 ASP cc_start: 0.8284 (p0) cc_final: 0.7810 (t0) REVERT: A 259 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8004 (tttm) REVERT: A 281 ARG cc_start: 0.7689 (ttp-170) cc_final: 0.7377 (mtt90) REVERT: B 88 ASP cc_start: 0.8285 (p0) cc_final: 0.7817 (t0) REVERT: B 259 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8013 (tttm) REVERT: B 281 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.7371 (mtt90) REVERT: C 88 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7841 (t0) REVERT: C 259 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8019 (tttm) REVERT: C 281 ARG cc_start: 0.7705 (ttp-170) cc_final: 0.7385 (mtt90) REVERT: D 88 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7844 (t0) REVERT: D 259 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8010 (tttm) REVERT: D 281 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7384 (mtt90) REVERT: E 278 GLU cc_start: 0.7804 (tt0) cc_final: 0.7394 (mp0) REVERT: G 278 GLU cc_start: 0.7794 (tt0) cc_final: 0.7395 (mp0) REVERT: G 327 ASP cc_start: 0.8120 (m-30) cc_final: 0.7894 (m-30) REVERT: H 327 ASP cc_start: 0.8122 (m-30) cc_final: 0.7895 (m-30) outliers start: 48 outliers final: 29 residues processed: 296 average time/residue: 0.8064 time to fit residues: 266.3638 Evaluate side-chains 305 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 362 GLU 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 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 362 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 362 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 10 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 83 optimal weight: 0.0040 chunk 119 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.123182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097467 restraints weight = 20594.656| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.43 r_work: 0.3170 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24728 Z= 0.195 Angle : 0.577 9.574 33520 Z= 0.308 Chirality : 0.049 0.231 3712 Planarity : 0.005 0.045 4440 Dihedral : 7.496 55.151 3712 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.72 % Allowed : 16.46 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.14), residues: 3136 helix: 1.38 (0.15), residues: 1288 sheet: 0.64 (0.30), residues: 296 loop : -1.13 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 50 TYR 0.016 0.002 TYR C 333 PHE 0.011 0.002 PHE B 229 TRP 0.007 0.001 TRP G 289 HIS 0.007 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00467 (24688) covalent geometry : angle 0.57685 (33504) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.25664 ( 16) hydrogen bonds : bond 0.05900 ( 1016) hydrogen bonds : angle 4.19556 ( 2832) metal coordination : bond 0.00434 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.609 Fit side-chains REVERT: A 88 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7837 (t0) REVERT: A 259 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8026 (tttm) REVERT: A 281 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7401 (mtt90) REVERT: B 88 ASP cc_start: 0.8298 (p0) cc_final: 0.7838 (t0) REVERT: B 259 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8043 (tttm) REVERT: B 281 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7400 (mtt90) REVERT: B 410 ASN cc_start: 0.8647 (m-40) cc_final: 0.8424 (m-40) REVERT: C 88 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7871 (t0) REVERT: C 259 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8058 (tttm) REVERT: C 281 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7401 (mtt90) REVERT: D 88 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7878 (t0) REVERT: D 259 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8029 (tttm) REVERT: D 281 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7403 (mtt90) REVERT: E 278 GLU cc_start: 0.7872 (tt0) cc_final: 0.7436 (mp0) REVERT: G 278 GLU cc_start: 0.7847 (tt0) cc_final: 0.7453 (mp0) REVERT: G 327 ASP cc_start: 0.8143 (m-30) cc_final: 0.7916 (m-30) REVERT: H 327 ASP cc_start: 0.8136 (m-30) cc_final: 0.7907 (m-30) outliers start: 42 outliers final: 31 residues processed: 284 average time/residue: 0.7752 time to fit residues: 246.8925 Evaluate side-chains 303 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 362 GLU 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 362 GLU 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 362 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 362 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 53 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 245 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.126250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100754 restraints weight = 21107.082| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.45 r_work: 0.3212 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24728 Z= 0.110 Angle : 0.491 9.480 33520 Z= 0.258 Chirality : 0.045 0.225 3712 Planarity : 0.004 0.040 4440 Dihedral : 6.457 51.867 3712 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.27 % Allowed : 16.99 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.15), residues: 3136 helix: 1.63 (0.15), residues: 1288 sheet: 0.70 (0.29), residues: 296 loop : -1.04 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 50 TYR 0.013 0.001 TYR C 333 PHE 0.007 0.001 PHE C 229 TRP 0.005 0.001 TRP E 289 HIS 0.007 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00244 (24688) covalent geometry : angle 0.49127 (33504) SS BOND : bond 0.00105 ( 8) SS BOND : angle 0.17278 ( 16) hydrogen bonds : bond 0.04159 ( 1016) hydrogen bonds : angle 3.93754 ( 2832) metal coordination : bond 0.00237 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 271 time to evaluate : 0.962 Fit side-chains REVERT: A 88 ASP cc_start: 0.8294 (p0) cc_final: 0.7803 (t0) REVERT: A 259 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7995 (tttm) REVERT: A 281 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7393 (mtt90) REVERT: B 88 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7794 (t0) REVERT: B 259 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7998 (tttm) REVERT: B 281 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7390 (mtt90) REVERT: C 88 ASP cc_start: 0.8304 (p0) cc_final: 0.7819 (t0) REVERT: C 259 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7998 (tttm) REVERT: C 281 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7398 (mtt90) REVERT: D 88 ASP cc_start: 0.8318 (p0) cc_final: 0.7827 (t0) REVERT: D 259 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7997 (tttm) REVERT: D 281 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7414 (mtt90) REVERT: E 278 GLU cc_start: 0.7774 (tt0) cc_final: 0.7378 (mp0) REVERT: G 278 GLU cc_start: 0.7776 (tt0) cc_final: 0.7380 (mp0) REVERT: G 327 ASP cc_start: 0.8145 (m-30) cc_final: 0.7923 (m-30) REVERT: H 327 ASP cc_start: 0.8153 (m-30) cc_final: 0.7945 (m-30) outliers start: 31 outliers final: 17 residues processed: 287 average time/residue: 0.7966 time to fit residues: 255.4435 Evaluate side-chains 295 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 362 GLU 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 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 141 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 208 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.124040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098339 restraints weight = 20805.283| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.45 r_work: 0.3182 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 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 : 0.004 0.031 24728 Z= 0.162 Angle : 0.548 11.510 33520 Z= 0.289 Chirality : 0.048 0.228 3712 Planarity : 0.005 0.040 4440 Dihedral : 7.100 52.183 3712 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.63 % Allowed : 16.34 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.14), residues: 3136 helix: 1.52 (0.15), residues: 1288 sheet: 0.70 (0.30), residues: 296 loop : -1.08 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 50 TYR 0.015 0.002 TYR C 333 PHE 0.009 0.001 PHE C 229 TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00382 (24688) covalent geometry : angle 0.54838 (33504) SS BOND : bond 0.00129 ( 8) SS BOND : angle 0.23649 ( 16) hydrogen bonds : bond 0.05304 ( 1016) hydrogen bonds : angle 4.09001 ( 2832) metal coordination : bond 0.00359 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8778.15 seconds wall clock time: 149 minutes 45.20 seconds (8985.20 seconds total)