Starting phenix.real_space_refine on Tue Sep 15 13:16:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6evw_3961/09_2026/6evw_3961.cif Found real_map, /net/cci-nas-00/data/ceres_data/6evw_3961/09_2026/6evw_3961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6evw_3961/09_2026/6evw_3961.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6evw_3961/09_2026/6evw_3961.cif" model { file = "/net/cci-nas-00/data/ceres_data/6evw_3961/09_2026/6evw_3961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6evw_3961/09_2026/6evw_3961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6evw_3961/09_2026/6evw_3961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6evw_3961/09_2026/6evw_3961.map" } resolution = 4.4 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= 0.013 sd= 0.039 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 P 36 5.49 5 Mg 12 5.21 5 S 276 5.16 5 C 25464 2.51 5 N 6918 2.21 5 O 7830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40536 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.88, per 1000 atoms: 0.19 Number of scatterers: 40536 At special positions: 0 Unit cell: (113.98, 169.58, 216.84, 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) S 276 16.00 P 36 15.00 Mg 12 11.99 O 7830 8.00 N 6918 7.00 C 25464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 36 sheets defined 49.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'E' and resid 10 through 28 removed outlier: 3.503A pdb=" N GLN E 15 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 removed outlier: 3.783A pdb=" N ASP E 76 " --> pdb=" O PRO E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 127 removed outlier: 3.720A pdb=" N VAL E 118 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 122 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.502A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.937A pdb=" N SER E 187 " --> pdb=" O GLU E 183 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU E 189 " --> pdb=" O TYR E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 195 Processing helix chain 'E' and resid 206 through 215 removed outlier: 3.787A pdb=" N TYR E 210 " --> pdb=" O ASN E 206 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.746A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 259 removed outlier: 3.717A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 removed outlier: 4.144A pdb=" N TYR E 282 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 4.018A pdb=" N THR E 292 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 removed outlier: 3.837A pdb=" N GLY E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.566A pdb=" N ALA E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.932A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 removed outlier: 4.050A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.875A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP E 424 " --> pdb=" O GLU E 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 426 " --> pdb=" O ARG E 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 removed outlier: 3.502A pdb=" N GLN J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU J 22 " --> pdb=" O ASN J 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 80 removed outlier: 3.783A pdb=" N ASP J 76 " --> pdb=" O PRO J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 114 through 127 removed outlier: 3.721A pdb=" N VAL J 118 " --> pdb=" O ILE J 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE J 122 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG J 123 " --> pdb=" O LEU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 161 removed outlier: 4.501A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 190 removed outlier: 3.938A pdb=" N SER J 187 " --> pdb=" O GLU J 183 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU J 189 " --> pdb=" O TYR J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 195 Processing helix chain 'J' and resid 206 through 215 removed outlier: 3.788A pdb=" N TYR J 210 " --> pdb=" O ASN J 206 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP J 211 " --> pdb=" O GLU J 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE J 212 " --> pdb=" O ALA J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 239 removed outlier: 3.746A pdb=" N ARG J 229 " --> pdb=" O THR J 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE J 231 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 259 removed outlier: 3.717A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 282 removed outlier: 4.143A pdb=" N TYR J 282 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 removed outlier: 4.017A pdb=" N THR J 292 " --> pdb=" O VAL J 288 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN J 293 " --> pdb=" O ALA J 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 310 removed outlier: 3.838A pdb=" N GLY J 310 " --> pdb=" O PRO J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 337 removed outlier: 3.566A pdb=" N ALA J 331 " --> pdb=" O ASP J 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE J 335 " --> pdb=" O ALA J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.932A pdb=" N TRP J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS J 394 " --> pdb=" O ARG J 390 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU J 397 " --> pdb=" O HIS J 393 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET J 398 " --> pdb=" O LYS J 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 409 removed outlier: 4.050A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 412 No H-bonds generated for 'chain 'J' and resid 410 through 412' Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.874A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER J 419 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU J 423 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP J 424 " --> pdb=" O GLU J 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET J 425 " --> pdb=" O ALA J 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA J 426 " --> pdb=" O ARG J 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP J 431 " --> pdb=" O ALA J 427 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.502A pdb=" N GLN C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 removed outlier: 3.783A pdb=" N ASP C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.720A pdb=" N VAL C 118 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 122 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.501A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.938A pdb=" N SER C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.788A pdb=" N TYR C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.747A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.717A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 4.143A pdb=" N TYR C 282 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.018A pdb=" N THR C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.837A pdb=" N GLY C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 337 removed outlier: 3.566A pdb=" N ALA C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.932A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.049A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.875A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 424 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 removed outlier: 3.502A pdb=" N GLN L 15 " --> pdb=" O GLN L 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 22 " --> pdb=" O ASN L 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 80 removed outlier: 3.783A pdb=" N ASP L 76 " --> pdb=" O PRO L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 114 through 127 removed outlier: 3.720A pdb=" N VAL L 118 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE L 122 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 161 removed outlier: 4.502A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL L 159 " --> pdb=" O GLU L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 190 removed outlier: 3.938A pdb=" N SER L 187 " --> pdb=" O GLU L 183 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU L 189 " --> pdb=" O TYR L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 195 Processing helix chain 'L' and resid 206 through 215 removed outlier: 3.787A pdb=" N TYR L 210 " --> pdb=" O ASN L 206 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP L 211 " --> pdb=" O GLU L 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE L 212 " --> pdb=" O ALA L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 239 removed outlier: 3.746A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE L 231 " --> pdb=" O LEU L 227 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 259 removed outlier: 3.717A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 282 removed outlier: 4.143A pdb=" N TYR L 282 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 4.017A pdb=" N THR L 292 " --> pdb=" O VAL L 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 310 removed outlier: 3.838A pdb=" N GLY L 310 " --> pdb=" O PRO L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 337 removed outlier: 3.566A pdb=" N ALA L 331 " --> pdb=" O ASP L 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.931A pdb=" N TRP L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA L 389 " --> pdb=" O ALA L 385 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS L 394 " --> pdb=" O ARG L 390 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU L 397 " --> pdb=" O HIS L 393 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET L 398 " --> pdb=" O LYS L 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 409 removed outlier: 4.050A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 412 No H-bonds generated for 'chain 'L' and resid 410 through 412' Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.875A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU L 423 " --> pdb=" O SER L 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP L 424 " --> pdb=" O GLU L 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET L 425 " --> pdb=" O ALA L 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA L 426 " --> pdb=" O ARG L 422 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP L 431 " --> pdb=" O ALA L 427 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.502A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.782A pdb=" N ASP A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.721A pdb=" N VAL A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.502A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.938A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.788A pdb=" N TYR A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.746A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.717A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 4.143A pdb=" N TYR A 282 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.017A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.837A pdb=" N GLY A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.566A pdb=" N ALA A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.932A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.050A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.875A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 removed outlier: 3.502A pdb=" N GLN K 15 " --> pdb=" O GLN K 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU K 22 " --> pdb=" O ASN K 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 80 removed outlier: 3.783A pdb=" N ASP K 76 " --> pdb=" O PRO K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 114 through 127 removed outlier: 3.720A pdb=" N VAL K 118 " --> pdb=" O ILE K 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE K 122 " --> pdb=" O VAL K 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG K 123 " --> pdb=" O LEU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 161 removed outlier: 4.502A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU K 152 " --> pdb=" O GLY K 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU K 157 " --> pdb=" O LEU K 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 190 removed outlier: 3.938A pdb=" N SER K 187 " --> pdb=" O GLU K 183 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE K 188 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU K 189 " --> pdb=" O TYR K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 195 Processing helix chain 'K' and resid 206 through 215 removed outlier: 3.788A pdb=" N TYR K 210 " --> pdb=" O ASN K 206 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP K 211 " --> pdb=" O GLU K 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE K 212 " --> pdb=" O ALA K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 239 removed outlier: 3.746A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 259 removed outlier: 3.717A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 282 removed outlier: 4.143A pdb=" N TYR K 282 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 4.017A pdb=" N THR K 292 " --> pdb=" O VAL K 288 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN K 293 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 310 removed outlier: 3.837A pdb=" N GLY K 310 " --> pdb=" O PRO K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 337 removed outlier: 3.566A pdb=" N ALA K 331 " --> pdb=" O ASP K 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.932A pdb=" N TRP K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA K 389 " --> pdb=" O ALA K 385 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS K 394 " --> pdb=" O ARG K 390 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU K 397 " --> pdb=" O HIS K 393 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET K 398 " --> pdb=" O LYS K 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 409 removed outlier: 4.050A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 412 No H-bonds generated for 'chain 'K' and resid 410 through 412' Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.876A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP K 424 " --> pdb=" O GLU K 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET K 425 " --> pdb=" O ALA K 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA K 426 " --> pdb=" O ARG K 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP K 431 " --> pdb=" O ALA K 427 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 27 removed outlier: 3.732A pdb=" N GLN B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.578A pdb=" N GLU B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.600A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 4.101A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 4.380A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.321A pdb=" N LEU B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 3.893A pdb=" N LEU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.927A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.702A pdb=" N ASN B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 299' Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.543A pdb=" N GLY B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 328 through 337 removed outlier: 3.822A pdb=" N VAL B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.531A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.555A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.924A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 27 removed outlier: 3.732A pdb=" N GLN F 15 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.578A pdb=" N GLU F 45 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 69 through 79 removed outlier: 4.600A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 108 through 127 removed outlier: 4.101A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 removed outlier: 4.382A pdb=" N GLY F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 196 removed outlier: 4.321A pdb=" N LEU F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN F 195 " --> pdb=" O GLN F 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 214 removed outlier: 3.894A pdb=" N LEU F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR F 214 " --> pdb=" O ILE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 226 through 237 removed outlier: 3.926A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 292 Processing helix chain 'F' and resid 295 through 299 removed outlier: 3.702A pdb=" N ASN F 298 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET F 299 " --> pdb=" O ALA F 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 295 through 299' Processing helix chain 'F' and resid 304 through 308 removed outlier: 3.544A pdb=" N GLY F 308 " --> pdb=" O PRO F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 328 through 337 removed outlier: 3.822A pdb=" N VAL F 333 " --> pdb=" O GLN F 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 388 removed outlier: 3.532A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG F 380 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET F 388 " --> pdb=" O GLN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 402 removed outlier: 4.554A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 428 removed outlier: 3.925A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN F 424 " --> pdb=" O SER F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 27 removed outlier: 3.732A pdb=" N GLN G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.579A pdb=" N GLU G 45 " --> pdb=" O ASP G 41 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 69 through 79 removed outlier: 4.600A pdb=" N MET G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 108 through 127 removed outlier: 4.101A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 159 removed outlier: 4.381A pdb=" N GLY G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER G 153 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 196 removed outlier: 4.321A pdb=" N LEU G 187 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU G 194 " --> pdb=" O HIS G 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN G 195 " --> pdb=" O GLN G 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR G 196 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 214 removed outlier: 3.894A pdb=" N LEU G 207 " --> pdb=" O ASP G 203 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR G 214 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 226 Processing helix chain 'G' and resid 226 through 237 removed outlier: 3.926A pdb=" N THR G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 285 through 292 Processing helix chain 'G' and resid 295 through 299 removed outlier: 3.703A pdb=" N ASN G 298 " --> pdb=" O ASP G 295 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET G 299 " --> pdb=" O ALA G 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 295 through 299' Processing helix chain 'G' and resid 304 through 308 removed outlier: 3.543A pdb=" N GLY G 308 " --> pdb=" O PRO G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 328 Processing helix chain 'G' and resid 328 through 337 removed outlier: 3.822A pdb=" N VAL G 333 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN G 337 " --> pdb=" O VAL G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 388 removed outlier: 3.531A pdb=" N PHE G 378 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG G 380 " --> pdb=" O GLU G 376 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET G 388 " --> pdb=" O GLN G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 402 removed outlier: 4.555A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 428 removed outlier: 3.924A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA G 411 " --> pdb=" O GLU G 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN G 424 " --> pdb=" O SER G 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 27 removed outlier: 3.733A pdb=" N GLN D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.578A pdb=" N GLU D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 69 through 79 removed outlier: 4.600A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 127 removed outlier: 4.101A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 4.381A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 4.320A pdb=" N LEU D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 removed outlier: 3.893A pdb=" N LEU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 214 " --> pdb=" O ILE D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 226 through 237 removed outlier: 3.927A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.702A pdb=" N ASN D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 299 " --> pdb=" O ALA D 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 295 through 299' Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.544A pdb=" N GLY D 308 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 328 through 337 removed outlier: 3.823A pdb=" N VAL D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 337 " --> pdb=" O VAL D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 removed outlier: 3.532A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 removed outlier: 4.554A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 428 removed outlier: 3.924A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 27 removed outlier: 3.733A pdb=" N GLN I 15 " --> pdb=" O GLN I 11 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.579A pdb=" N GLU I 45 " --> pdb=" O ASP I 41 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 69 through 79 removed outlier: 4.600A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 127 removed outlier: 4.101A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 removed outlier: 4.381A pdb=" N GLY I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER I 153 " --> pdb=" O THR I 149 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS I 154 " --> pdb=" O LEU I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 4.321A pdb=" N LEU I 187 " --> pdb=" O TYR I 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER I 188 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN I 195 " --> pdb=" O GLN I 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR I 196 " --> pdb=" O LEU I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 removed outlier: 3.893A pdb=" N LEU I 207 " --> pdb=" O ASP I 203 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR I 214 " --> pdb=" O ILE I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 226 Processing helix chain 'I' and resid 226 through 237 removed outlier: 3.927A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 285 through 292 Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.702A pdb=" N ASN I 298 " --> pdb=" O ASP I 295 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET I 299 " --> pdb=" O ALA I 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 295 through 299' Processing helix chain 'I' and resid 304 through 308 removed outlier: 3.544A pdb=" N GLY I 308 " --> pdb=" O PRO I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 328 Processing helix chain 'I' and resid 328 through 337 removed outlier: 3.822A pdb=" N VAL I 333 " --> pdb=" O GLN I 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN I 335 " --> pdb=" O LEU I 331 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN I 337 " --> pdb=" O VAL I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 388 removed outlier: 3.531A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG I 380 " --> pdb=" O GLU I 376 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET I 388 " --> pdb=" O GLN I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 402 removed outlier: 4.555A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 428 removed outlier: 3.925A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA I 411 " --> pdb=" O GLU I 407 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN I 424 " --> pdb=" O SER I 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 27 removed outlier: 3.732A pdb=" N GLN H 15 " --> pdb=" O GLN H 11 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.579A pdb=" N GLU H 45 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 46' Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 69 through 79 removed outlier: 4.600A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 127 removed outlier: 4.101A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 removed outlier: 4.381A pdb=" N GLY H 148 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER H 153 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 196 removed outlier: 4.320A pdb=" N LEU H 187 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER H 188 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 195 " --> pdb=" O GLN H 191 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR H 196 " --> pdb=" O LEU H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 214 removed outlier: 3.894A pdb=" N LEU H 207 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 226 Processing helix chain 'H' and resid 226 through 237 removed outlier: 3.926A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 258 Processing helix chain 'H' and resid 285 through 292 Processing helix chain 'H' and resid 295 through 299 removed outlier: 3.702A pdb=" N ASN H 298 " --> pdb=" O ASP H 295 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET H 299 " --> pdb=" O ALA H 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 295 through 299' Processing helix chain 'H' and resid 304 through 308 removed outlier: 3.544A pdb=" N GLY H 308 " --> pdb=" O PRO H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 328 Processing helix chain 'H' and resid 328 through 337 removed outlier: 3.822A pdb=" N VAL H 333 " --> pdb=" O GLN H 329 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN H 335 " --> pdb=" O LEU H 331 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN H 337 " --> pdb=" O VAL H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 388 removed outlier: 3.531A pdb=" N PHE H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG H 380 " --> pdb=" O GLU H 376 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 402 removed outlier: 4.554A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 428 removed outlier: 3.925A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA H 411 " --> pdb=" O GLU H 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN H 424 " --> pdb=" O SER H 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.412A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 5 " --> pdb=" O GLY E 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'E' and resid 167 through 169 removed outlier: 6.688A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 270 through 273 Processing sheet with id=AA5, first strand: chain 'J' and resid 65 through 68 removed outlier: 6.412A pdb=" N GLU J 3 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY J 134 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE J 5 " --> pdb=" O GLY J 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'J' and resid 167 through 169 removed outlier: 6.689A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'J' and resid 270 through 273 Processing sheet with id=AA9, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.412A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 5 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'C' and resid 167 through 169 removed outlier: 6.689A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 270 through 273 Processing sheet with id=AB4, first strand: chain 'L' and resid 65 through 68 removed outlier: 6.412A pdb=" N GLU L 3 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY L 134 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 5 " --> pdb=" O GLY L 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'L' and resid 167 through 169 removed outlier: 6.688A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 270 through 273 Processing sheet with id=AB8, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.412A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 5 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.688A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 270 through 273 Processing sheet with id=AC3, first strand: chain 'K' and resid 65 through 68 removed outlier: 6.412A pdb=" N GLU K 3 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY K 134 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE K 5 " --> pdb=" O GLY K 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'K' and resid 167 through 169 removed outlier: 6.688A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'K' and resid 270 through 273 Processing sheet with id=AC7, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.749A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 66 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AC9, first strand: chain 'F' and resid 90 through 92 removed outlier: 7.749A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL F 66 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE F 202 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER F 168 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N CYS F 201 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N PHE F 270 " --> pdb=" O CYS F 201 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR F 312 " --> pdb=" O ASN F 370 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N LYS F 350 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL F 313 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA F 352 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA F 315 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N CYS F 354 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE F 317 " --> pdb=" O CYS F 354 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=AD2, first strand: chain 'G' and resid 90 through 92 removed outlier: 7.749A pdb=" N VAL G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU G 65 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL G 66 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN G 165 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE G 133 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL G 169 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE G 202 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER G 168 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N CYS G 201 " --> pdb=" O PRO G 268 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N PHE G 270 " --> pdb=" O CYS G 201 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR G 312 " --> pdb=" O ASN G 370 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=AD4, first strand: chain 'D' and resid 90 through 92 removed outlier: 7.749A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 66 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 51 through 52 Processing sheet with id=AD6, first strand: chain 'I' and resid 90 through 92 removed outlier: 7.749A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL I 66 " --> pdb=" O GLN I 8 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE I 202 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR I 312 " --> pdb=" O ASN I 370 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 51 through 52 Processing sheet with id=AD8, first strand: chain 'H' and resid 90 through 92 removed outlier: 7.748A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL H 66 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN H 165 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL H 169 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE H 202 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER H 168 " --> pdb=" O ILE H 202 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N CYS H 201 " --> pdb=" O PRO H 268 " (cutoff:3.500A) removed outlier: 11.447A pdb=" N PHE H 270 " --> pdb=" O CYS H 201 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR H 312 " --> pdb=" O ASN H 370 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 51 through 52 1411 hydrogen bonds defined for protein. 4107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13215 1.34 - 1.46: 7322 1.46 - 1.57: 20437 1.57 - 1.69: 36 1.69 - 1.81: 444 Bond restraints: 41454 Sorted by residual: bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.590 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" O3B G2P G 501 " pdb=" PG G2P G 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 41449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 55153 2.38 - 4.76: 971 4.76 - 7.13: 115 7.13 - 9.51: 69 9.51 - 11.89: 20 Bond angle restraints: 56328 Sorted by residual: angle pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " pdb=" PB GTP L 501 " ideal model delta sigma weight residual 120.50 132.39 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " pdb=" PB GTP C 501 " ideal model delta sigma weight residual 120.50 132.05 -11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sigma weight residual 120.50 131.99 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " pdb=" PB GTP K 501 " ideal model delta sigma weight residual 120.50 131.95 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " pdb=" PB GTP E 501 " ideal model delta sigma weight residual 120.50 131.66 -11.16 3.00e+00 1.11e-01 1.38e+01 ... (remaining 56323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 24391 34.54 - 69.08: 149 69.08 - 103.62: 30 103.62 - 138.16: 0 138.16 - 172.70: 18 Dihedral angle restraints: 24588 sinusoidal: 9804 harmonic: 14784 Sorted by residual: dihedral pdb=" C8 GTP L 501 " pdb=" C1' GTP L 501 " pdb=" N9 GTP L 501 " pdb=" O4' GTP L 501 " ideal model delta sinusoidal sigma weight residual 104.59 -68.10 172.70 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP J 501 " pdb=" C1' GTP J 501 " pdb=" N9 GTP J 501 " pdb=" O4' GTP J 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.62 172.22 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP K 501 " pdb=" C1' GTP K 501 " pdb=" N9 GTP K 501 " pdb=" O4' GTP K 501 " ideal model delta sinusoidal sigma weight residual 104.59 -66.88 171.47 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 24585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4131 0.045 - 0.091: 1544 0.091 - 0.136: 433 0.136 - 0.182: 24 0.182 - 0.227: 30 Chirality restraints: 6162 Sorted by residual: chirality pdb=" C2' GTP C 501 " pdb=" C1' GTP C 501 " pdb=" C3' GTP C 501 " pdb=" O2' GTP C 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C2' GTP A 501 " pdb=" C1' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" O2' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2' GTP J 501 " pdb=" C1' GTP J 501 " pdb=" C3' GTP J 501 " pdb=" O2' GTP J 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 6159 not shown) Planarity restraints: 7326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G2P G 501 " 0.119 2.00e-02 2.50e+03 4.92e-02 7.27e+01 pdb=" C2 G2P G 501 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G2P G 501 " -0.040 2.00e-02 2.50e+03 pdb=" C5 G2P G 501 " -0.035 2.00e-02 2.50e+03 pdb=" C6 G2P G 501 " 0.013 2.00e-02 2.50e+03 pdb=" C8 G2P G 501 " -0.035 2.00e-02 2.50e+03 pdb=" N1 G2P G 501 " 0.018 2.00e-02 2.50e+03 pdb=" N2 G2P G 501 " -0.011 2.00e-02 2.50e+03 pdb=" N3 G2P G 501 " -0.039 2.00e-02 2.50e+03 pdb=" N7 G2P G 501 " -0.043 2.00e-02 2.50e+03 pdb=" N9 G2P G 501 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G2P G 501 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G2P I 501 " -0.119 2.00e-02 2.50e+03 4.91e-02 7.22e+01 pdb=" C2 G2P I 501 " 0.012 2.00e-02 2.50e+03 pdb=" C4 G2P I 501 " 0.043 2.00e-02 2.50e+03 pdb=" C5 G2P I 501 " 0.036 2.00e-02 2.50e+03 pdb=" C6 G2P I 501 " -0.013 2.00e-02 2.50e+03 pdb=" C8 G2P I 501 " 0.032 2.00e-02 2.50e+03 pdb=" N1 G2P I 501 " -0.020 2.00e-02 2.50e+03 pdb=" N2 G2P I 501 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G2P I 501 " 0.043 2.00e-02 2.50e+03 pdb=" N7 G2P I 501 " 0.041 2.00e-02 2.50e+03 pdb=" N9 G2P I 501 " 0.016 2.00e-02 2.50e+03 pdb=" O6 G2P I 501 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G2P D 501 " -0.118 2.00e-02 2.50e+03 4.87e-02 7.13e+01 pdb=" C2 G2P D 501 " 0.013 2.00e-02 2.50e+03 pdb=" C4 G2P D 501 " 0.042 2.00e-02 2.50e+03 pdb=" C5 G2P D 501 " 0.035 2.00e-02 2.50e+03 pdb=" C6 G2P D 501 " -0.014 2.00e-02 2.50e+03 pdb=" C8 G2P D 501 " 0.033 2.00e-02 2.50e+03 pdb=" N1 G2P D 501 " -0.019 2.00e-02 2.50e+03 pdb=" N2 G2P D 501 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G2P D 501 " 0.042 2.00e-02 2.50e+03 pdb=" N7 G2P D 501 " 0.040 2.00e-02 2.50e+03 pdb=" N9 G2P D 501 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G2P D 501 " -0.078 2.00e-02 2.50e+03 ... (remaining 7323 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 656 2.65 - 3.21: 36586 3.21 - 3.78: 62604 3.78 - 4.34: 88246 4.34 - 4.90: 139919 Nonbonded interactions: 328011 Sorted by model distance: nonbonded pdb=" O2B GTP C 501 " pdb="MG MG C 502 " model vdw 2.091 2.170 nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.092 2.170 nonbonded pdb=" O2B GTP J 501 " pdb="MG MG J 502 " model vdw 2.095 2.170 nonbonded pdb=" OE1 GLN G 11 " pdb="MG MG G 502 " model vdw 2.099 2.170 nonbonded pdb=" O1B G2P G 501 " pdb="MG MG G 502 " model vdw 2.101 2.170 ... (remaining 328006 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: 0.14 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'C' selection = chain 'L' selection = chain 'A' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'D' selection = chain 'I' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 35.940 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.005 0.126 41454 Z= 0.241 Angle : 0.838 11.892 56328 Z= 0.431 Chirality : 0.051 0.227 6162 Planarity : 0.006 0.056 7326 Dihedral : 11.286 172.697 15096 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.53 (0.09), residues: 5064 helix: -3.66 (0.06), residues: 2052 sheet: -1.81 (0.18), residues: 762 loop : -2.64 (0.11), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 318 TYR 0.022 0.002 TYR K 24 PHE 0.018 0.002 PHE J 202 TRP 0.022 0.003 TRP G 101 HIS 0.010 0.002 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.24 (41454) covalent geometry : angle 0.83835 / 0.43 (56328) hydrogen bonds : bond 0.30830 / 20.26 ( 1411) hydrogen bonds : angle 9.50907 / 6.65 ( 4107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1439 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7252 (ptm) cc_final: 0.6367 (tmm) REVERT: E 120 ASP cc_start: 0.8512 (t70) cc_final: 0.8276 (t70) REVERT: E 172 TYR cc_start: 0.7728 (t80) cc_final: 0.6354 (t80) REVERT: E 192 HIS cc_start: 0.7682 (t-90) cc_final: 0.7333 (t-90) REVERT: E 205 ASP cc_start: 0.7674 (t0) cc_final: 0.6236 (m-30) REVERT: E 301 GLN cc_start: 0.8369 (mt0) cc_final: 0.8164 (mt0) REVERT: E 302 MET cc_start: 0.8303 (mtt) cc_final: 0.7994 (mtt) REVERT: E 313 MET cc_start: 0.8051 (mtm) cc_final: 0.6800 (ttt) REVERT: E 351 PHE cc_start: 0.8166 (m-80) cc_final: 0.7375 (m-80) REVERT: E 391 LEU cc_start: 0.9167 (tp) cc_final: 0.8793 (tp) REVERT: E 398 MET cc_start: 0.7518 (mtp) cc_final: 0.7195 (mtm) REVERT: E 425 MET cc_start: 0.8679 (tpp) cc_final: 0.7971 (mmm) REVERT: J 124 LYS cc_start: 0.8316 (mttm) cc_final: 0.8024 (tptp) REVERT: J 149 PHE cc_start: 0.8577 (t80) cc_final: 0.8268 (t80) REVERT: J 172 TYR cc_start: 0.7670 (t80) cc_final: 0.6198 (t80) REVERT: J 205 ASP cc_start: 0.7452 (t0) cc_final: 0.6339 (m-30) REVERT: J 221 ARG cc_start: 0.8700 (mtt90) cc_final: 0.8448 (mpp-170) REVERT: J 267 PHE cc_start: 0.9043 (m-80) cc_final: 0.8743 (m-80) REVERT: J 313 MET cc_start: 0.7410 (mtm) cc_final: 0.6305 (ttt) REVERT: J 316 CYS cc_start: 0.8439 (t) cc_final: 0.7768 (t) REVERT: J 391 LEU cc_start: 0.9118 (tp) cc_final: 0.8711 (tp) REVERT: J 398 MET cc_start: 0.7304 (mtp) cc_final: 0.7023 (mtm) REVERT: J 425 MET cc_start: 0.8545 (tpp) cc_final: 0.7898 (mmm) REVERT: C 24 TYR cc_start: 0.8374 (m-80) cc_final: 0.8158 (m-80) REVERT: C 36 MET cc_start: 0.7276 (ptm) cc_final: 0.6608 (tmm) REVERT: C 149 PHE cc_start: 0.7882 (t80) cc_final: 0.7579 (t80) REVERT: C 182 VAL cc_start: 0.8535 (m) cc_final: 0.7966 (p) REVERT: C 192 HIS cc_start: 0.8136 (t-90) cc_final: 0.7857 (t-90) REVERT: C 205 ASP cc_start: 0.8280 (t0) cc_final: 0.6862 (m-30) REVERT: C 212 ILE cc_start: 0.8999 (mt) cc_final: 0.8798 (mm) REVERT: C 301 GLN cc_start: 0.8446 (mt0) cc_final: 0.8049 (pt0) REVERT: C 313 MET cc_start: 0.7803 (mtm) cc_final: 0.6520 (ttt) REVERT: C 377 MET cc_start: 0.7876 (ttp) cc_final: 0.7421 (tmm) REVERT: C 425 MET cc_start: 0.8389 (tpp) cc_final: 0.7630 (mmm) REVERT: L 36 MET cc_start: 0.7183 (ptm) cc_final: 0.6234 (tmm) REVERT: L 136 LEU cc_start: 0.8800 (mt) cc_final: 0.8516 (mp) REVERT: L 149 PHE cc_start: 0.8299 (t80) cc_final: 0.8050 (t80) REVERT: L 205 ASP cc_start: 0.8002 (t0) cc_final: 0.6435 (m-30) REVERT: L 301 GLN cc_start: 0.8678 (mt0) cc_final: 0.8004 (pt0) REVERT: L 313 MET cc_start: 0.7719 (mtm) cc_final: 0.6379 (mtp) REVERT: L 377 MET cc_start: 0.7485 (ttp) cc_final: 0.7245 (tmm) REVERT: L 395 PHE cc_start: 0.8848 (t80) cc_final: 0.8164 (t80) REVERT: L 425 MET cc_start: 0.8511 (tpp) cc_final: 0.7620 (mmm) REVERT: A 24 TYR cc_start: 0.8486 (m-80) cc_final: 0.8277 (m-80) REVERT: A 36 MET cc_start: 0.7028 (ptm) cc_final: 0.6398 (tmm) REVERT: A 54 SER cc_start: 0.7385 (p) cc_final: 0.6875 (t) REVERT: A 149 PHE cc_start: 0.8296 (t80) cc_final: 0.8060 (t80) REVERT: A 172 TYR cc_start: 0.7521 (t80) cc_final: 0.6307 (t80) REVERT: A 182 VAL cc_start: 0.8502 (m) cc_final: 0.7817 (p) REVERT: A 196 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8060 (tm-30) REVERT: A 205 ASP cc_start: 0.8003 (t0) cc_final: 0.6278 (m-30) REVERT: A 260 VAL cc_start: 0.8860 (t) cc_final: 0.8621 (t) REVERT: A 267 PHE cc_start: 0.8917 (m-80) cc_final: 0.8551 (m-80) REVERT: A 377 MET cc_start: 0.7915 (ttp) cc_final: 0.7216 (tmm) REVERT: A 380 ASN cc_start: 0.8414 (t0) cc_final: 0.8046 (t0) REVERT: A 391 LEU cc_start: 0.9095 (tp) cc_final: 0.8800 (tp) REVERT: A 398 MET cc_start: 0.7276 (mtp) cc_final: 0.6713 (mtm) REVERT: K 36 MET cc_start: 0.7261 (ptm) cc_final: 0.6636 (tmm) REVERT: K 136 LEU cc_start: 0.8480 (mt) cc_final: 0.8096 (mp) REVERT: K 149 PHE cc_start: 0.8319 (t80) cc_final: 0.7914 (t80) REVERT: K 172 TYR cc_start: 0.7755 (t80) cc_final: 0.6494 (t80) REVERT: K 205 ASP cc_start: 0.8220 (t0) cc_final: 0.6362 (m-30) REVERT: K 212 ILE cc_start: 0.9261 (mt) cc_final: 0.8941 (mt) REVERT: K 316 CYS cc_start: 0.8287 (t) cc_final: 0.7312 (t) REVERT: K 319 TYR cc_start: 0.8184 (m-80) cc_final: 0.7958 (m-10) REVERT: K 377 MET cc_start: 0.7564 (ttp) cc_final: 0.7317 (tmm) REVERT: B 14 ASN cc_start: 0.8491 (m-40) cc_final: 0.8258 (t0) REVERT: B 51 TYR cc_start: 0.8071 (m-80) cc_final: 0.7639 (m-10) REVERT: B 163 ILE cc_start: 0.8678 (pp) cc_final: 0.8215 (mt) REVERT: B 181 GLU cc_start: 0.8937 (pt0) cc_final: 0.8522 (pp20) REVERT: B 200 TYR cc_start: 0.7995 (m-80) cc_final: 0.7528 (m-80) REVERT: B 293 MET cc_start: 0.7126 (mtm) cc_final: 0.6759 (mmm) REVERT: B 297 LYS cc_start: 0.8754 (ptpt) cc_final: 0.8515 (mtmm) REVERT: B 317 PHE cc_start: 0.8738 (m-80) cc_final: 0.8498 (m-80) REVERT: B 355 ASP cc_start: 0.8482 (m-30) cc_final: 0.8113 (m-30) REVERT: B 379 LYS cc_start: 0.8918 (mtpt) cc_final: 0.7758 (pttp) REVERT: B 383 GLU cc_start: 0.8980 (tt0) cc_final: 0.8743 (mm-30) REVERT: F 6 HIS cc_start: 0.8754 (t70) cc_final: 0.8079 (t-170) REVERT: F 51 TYR cc_start: 0.7823 (m-80) cc_final: 0.7391 (m-10) REVERT: F 117 LEU cc_start: 0.8072 (mt) cc_final: 0.7866 (mm) REVERT: F 163 ILE cc_start: 0.8709 (pp) cc_final: 0.7899 (tp) REVERT: F 197 ASP cc_start: 0.7853 (m-30) cc_final: 0.7640 (m-30) REVERT: F 210 ILE cc_start: 0.9025 (mt) cc_final: 0.8766 (tt) REVERT: F 216 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7792 (mmtm) REVERT: F 233 MET cc_start: 0.9393 (mtp) cc_final: 0.8956 (mtm) REVERT: F 330 MET cc_start: 0.8434 (mmp) cc_final: 0.8107 (mmm) REVERT: F 379 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8613 (pttp) REVERT: G 73 MET cc_start: 0.8235 (mmt) cc_final: 0.8013 (mmt) REVERT: G 163 ILE cc_start: 0.8653 (pp) cc_final: 0.7950 (mt) REVERT: G 178 THR cc_start: 0.8475 (m) cc_final: 0.8245 (m) REVERT: G 233 MET cc_start: 0.9306 (mtp) cc_final: 0.8831 (mtm) REVERT: G 288 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7597 (tm-30) REVERT: G 332 ASN cc_start: 0.8023 (t0) cc_final: 0.7705 (p0) REVERT: G 379 LYS cc_start: 0.9137 (mtpt) cc_final: 0.8511 (pttp) REVERT: D 6 HIS cc_start: 0.8701 (t70) cc_final: 0.8135 (t70) REVERT: D 14 ASN cc_start: 0.8421 (m-40) cc_final: 0.8165 (t0) REVERT: D 21 TRP cc_start: 0.8777 (m100) cc_final: 0.8278 (m100) REVERT: D 51 TYR cc_start: 0.8049 (m-80) cc_final: 0.7151 (m-10) REVERT: D 163 ILE cc_start: 0.8814 (pp) cc_final: 0.8227 (mt) REVERT: D 181 GLU cc_start: 0.8928 (pt0) cc_final: 0.8642 (pp20) REVERT: D 200 TYR cc_start: 0.8095 (m-80) cc_final: 0.7147 (m-80) REVERT: D 293 MET cc_start: 0.7408 (mtm) cc_final: 0.6883 (mmm) REVERT: D 317 PHE cc_start: 0.8794 (m-80) cc_final: 0.8540 (m-80) REVERT: D 355 ASP cc_start: 0.8403 (m-30) cc_final: 0.8099 (m-30) REVERT: D 379 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8827 (mtmm) REVERT: I 14 ASN cc_start: 0.8403 (m-40) cc_final: 0.8069 (t0) REVERT: I 163 ILE cc_start: 0.8943 (pp) cc_final: 0.8342 (mt) REVERT: I 200 TYR cc_start: 0.7981 (m-80) cc_final: 0.7534 (m-80) REVERT: I 242 PHE cc_start: 0.7765 (m-80) cc_final: 0.7554 (m-10) REVERT: I 250 LEU cc_start: 0.8634 (mt) cc_final: 0.8399 (mp) REVERT: I 297 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7713 (mmtm) REVERT: I 353 VAL cc_start: 0.8735 (t) cc_final: 0.8526 (p) REVERT: I 379 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8885 (mttp) REVERT: H 6 HIS cc_start: 0.8621 (t70) cc_final: 0.8002 (t70) REVERT: H 85 PHE cc_start: 0.8575 (m-80) cc_final: 0.8294 (m-10) REVERT: H 163 ILE cc_start: 0.8682 (pp) cc_final: 0.8226 (mt) REVERT: H 216 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8370 (mtmm) REVERT: H 242 PHE cc_start: 0.8071 (m-80) cc_final: 0.7683 (m-10) REVERT: H 293 MET cc_start: 0.7373 (mtm) cc_final: 0.6908 (mmm) REVERT: H 297 LYS cc_start: 0.8357 (ptpt) cc_final: 0.8156 (mmtm) REVERT: H 332 ASN cc_start: 0.7871 (t0) cc_final: 0.7576 (p0) REVERT: H 379 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8518 (mttt) outliers start: 0 outliers final: 0 residues processed: 1439 average time/residue: 0.2600 time to fit residues: 604.3049 Evaluate side-chains 713 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 713 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 0.2980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 overall best weight: 7.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 28 HIS ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 258 ASN E 300 ASN E 380 ASN J 28 HIS ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS ** J 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 HIS J 300 ASN J 372 GLN C 28 HIS ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 258 ASN L 28 HIS ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS A 28 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 258 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 256 ASN B 291 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS B 423 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 131 GLN F 256 ASN F 292 GLN F 337 ASN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 HIS F 423 GLN G 131 GLN G 256 ASN G 292 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 256 ASN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN I 184 ASN I 256 ASN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN H 256 ASN H 291 GLN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.095689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084988 restraints weight = 126267.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.087640 restraints weight = 72894.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.089489 restraints weight = 46619.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.090779 restraints weight = 31957.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.091689 restraints weight = 23150.481| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 41454 Z= 0.201 Angle : 0.653 8.113 56328 Z= 0.348 Chirality : 0.045 0.155 6162 Planarity : 0.005 0.055 7326 Dihedral : 12.035 176.280 5658 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.10), residues: 5064 helix: -2.01 (0.09), residues: 2166 sheet: -1.21 (0.19), residues: 714 loop : -2.10 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 422 TYR 0.032 0.002 TYR J 108 PHE 0.036 0.002 PHE D 212 TRP 0.025 0.002 TRP F 101 HIS 0.015 0.002 HIS J 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (41454) covalent geometry : angle 0.65296 / 0.35 (56328) hydrogen bonds : bond 0.05386 / 3.57 ( 1411) hydrogen bonds : angle 5.78164 / 4.06 ( 4107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 975 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 16 ILE cc_start: 0.9282 (mt) cc_final: 0.9020 (mm) REVERT: E 36 MET cc_start: 0.7041 (ptm) cc_final: 0.6262 (tmm) REVERT: E 54 SER cc_start: 0.7431 (p) cc_final: 0.7122 (t) REVERT: E 123 ARG cc_start: 0.8606 (mtm-85) cc_final: 0.8068 (mtp85) REVERT: E 135 PHE cc_start: 0.8837 (m-80) cc_final: 0.8305 (m-10) REVERT: E 136 LEU cc_start: 0.8781 (mp) cc_final: 0.8464 (mm) REVERT: E 205 ASP cc_start: 0.7261 (t0) cc_final: 0.6232 (m-30) REVERT: E 213 CYS cc_start: 0.8610 (t) cc_final: 0.8386 (t) REVERT: E 250 VAL cc_start: 0.7905 (t) cc_final: 0.7657 (t) REVERT: E 267 PHE cc_start: 0.9070 (m-80) cc_final: 0.8818 (m-80) REVERT: E 313 MET cc_start: 0.7990 (mtm) cc_final: 0.6745 (mtp) REVERT: E 413 MET cc_start: 0.8162 (mmt) cc_final: 0.7956 (mmm) REVERT: J 14 VAL cc_start: 0.9212 (t) cc_final: 0.8941 (p) REVERT: J 16 ILE cc_start: 0.9166 (mt) cc_final: 0.8919 (mt) REVERT: J 24 TYR cc_start: 0.8236 (m-80) cc_final: 0.7970 (m-80) REVERT: J 124 LYS cc_start: 0.8475 (mttm) cc_final: 0.8086 (tptp) REVERT: J 149 PHE cc_start: 0.8509 (t80) cc_final: 0.8154 (t80) REVERT: J 195 LEU cc_start: 0.7883 (mm) cc_final: 0.7511 (mm) REVERT: J 205 ASP cc_start: 0.7543 (t0) cc_final: 0.6614 (m-30) REVERT: J 260 VAL cc_start: 0.8804 (t) cc_final: 0.8412 (p) REVERT: J 267 PHE cc_start: 0.9114 (m-80) cc_final: 0.8839 (m-80) REVERT: J 313 MET cc_start: 0.7681 (mtm) cc_final: 0.6397 (mtp) REVERT: J 388 TRP cc_start: 0.7960 (m-10) cc_final: 0.7703 (m-10) REVERT: C 36 MET cc_start: 0.6648 (ptm) cc_final: 0.6097 (tmm) REVERT: C 149 PHE cc_start: 0.7971 (t80) cc_final: 0.7547 (t80) REVERT: C 205 ASP cc_start: 0.7445 (t0) cc_final: 0.6934 (m-30) REVERT: C 301 GLN cc_start: 0.8766 (mt0) cc_final: 0.8186 (pt0) REVERT: C 313 MET cc_start: 0.7800 (mtm) cc_final: 0.6678 (mtp) REVERT: C 377 MET cc_start: 0.7967 (ttp) cc_final: 0.7341 (tmm) REVERT: L 36 MET cc_start: 0.6733 (ptm) cc_final: 0.6266 (tmm) REVERT: L 136 LEU cc_start: 0.8910 (mt) cc_final: 0.8597 (mp) REVERT: L 149 PHE cc_start: 0.8372 (t80) cc_final: 0.7926 (t80) REVERT: L 183 GLU cc_start: 0.7720 (pm20) cc_final: 0.7446 (pm20) REVERT: L 195 LEU cc_start: 0.8025 (mm) cc_final: 0.7789 (mm) REVERT: L 205 ASP cc_start: 0.7709 (t0) cc_final: 0.6717 (m-30) REVERT: L 256 GLN cc_start: 0.8208 (pt0) cc_final: 0.7692 (tt0) REVERT: L 301 GLN cc_start: 0.8789 (mt0) cc_final: 0.8195 (pt0) REVERT: L 313 MET cc_start: 0.7543 (mtm) cc_final: 0.6209 (mtp) REVERT: L 377 MET cc_start: 0.7344 (ttp) cc_final: 0.6682 (tmm) REVERT: L 395 PHE cc_start: 0.8967 (t80) cc_final: 0.8438 (t80) REVERT: A 36 MET cc_start: 0.6404 (ptm) cc_final: 0.5793 (tmm) REVERT: A 119 LEU cc_start: 0.9182 (mt) cc_final: 0.8898 (mm) REVERT: A 149 PHE cc_start: 0.8061 (t80) cc_final: 0.7667 (t80) REVERT: A 183 GLU cc_start: 0.7903 (pp20) cc_final: 0.7664 (pp20) REVERT: A 205 ASP cc_start: 0.7229 (t0) cc_final: 0.6436 (m-30) REVERT: A 267 PHE cc_start: 0.9116 (m-80) cc_final: 0.8753 (m-80) REVERT: A 377 MET cc_start: 0.7591 (ttp) cc_final: 0.7018 (tmm) REVERT: K 14 VAL cc_start: 0.9111 (t) cc_final: 0.8896 (p) REVERT: K 36 MET cc_start: 0.6921 (ptm) cc_final: 0.6067 (tmm) REVERT: K 54 SER cc_start: 0.7196 (p) cc_final: 0.6820 (t) REVERT: K 149 PHE cc_start: 0.8218 (t80) cc_final: 0.7857 (t80) REVERT: K 205 ASP cc_start: 0.7055 (t0) cc_final: 0.6283 (m-30) REVERT: K 267 PHE cc_start: 0.9016 (m-80) cc_final: 0.8672 (m-80) REVERT: K 301 GLN cc_start: 0.8224 (mt0) cc_final: 0.7660 (pt0) REVERT: K 315 CYS cc_start: 0.9050 (t) cc_final: 0.8632 (t) REVERT: K 316 CYS cc_start: 0.7938 (t) cc_final: 0.7141 (t) REVERT: B 43 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6514 (tm-30) REVERT: B 51 TYR cc_start: 0.7895 (m-80) cc_final: 0.7286 (m-10) REVERT: B 163 ILE cc_start: 0.8881 (pt) cc_final: 0.8175 (mt) REVERT: B 181 GLU cc_start: 0.8976 (pt0) cc_final: 0.8473 (pp20) REVERT: B 297 LYS cc_start: 0.8963 (ptpt) cc_final: 0.8684 (mtmm) REVERT: B 403 MET cc_start: 0.6889 (mtt) cc_final: 0.6643 (mtt) REVERT: F 51 TYR cc_start: 0.7860 (m-80) cc_final: 0.7017 (m-10) REVERT: F 85 PHE cc_start: 0.8161 (m-80) cc_final: 0.7608 (m-80) REVERT: F 163 ILE cc_start: 0.8540 (pt) cc_final: 0.8008 (mt) REVERT: F 197 ASP cc_start: 0.8007 (m-30) cc_final: 0.7726 (t70) REVERT: F 216 LYS cc_start: 0.8309 (mmtp) cc_final: 0.7890 (mmtm) REVERT: F 233 MET cc_start: 0.9169 (mtp) cc_final: 0.8825 (mtm) REVERT: F 242 PHE cc_start: 0.8015 (m-80) cc_final: 0.7388 (m-10) REVERT: F 250 LEU cc_start: 0.8535 (mt) cc_final: 0.7932 (mp) REVERT: F 253 LEU cc_start: 0.9320 (mt) cc_final: 0.8847 (pp) REVERT: F 267 MET cc_start: 0.7472 (mtm) cc_final: 0.7048 (mtm) REVERT: F 300 MET cc_start: 0.8714 (mtt) cc_final: 0.8377 (mtm) REVERT: G 50 TYR cc_start: 0.7552 (m-10) cc_final: 0.7351 (m-10) REVERT: G 83 GLN cc_start: 0.8454 (mp10) cc_final: 0.7845 (mm110) REVERT: G 233 MET cc_start: 0.9139 (mtp) cc_final: 0.8792 (mtm) REVERT: G 257 MET cc_start: 0.8658 (mtm) cc_final: 0.8450 (mtt) REVERT: G 328 GLU cc_start: 0.8321 (tp30) cc_final: 0.8030 (tp30) REVERT: G 332 ASN cc_start: 0.7845 (t0) cc_final: 0.7585 (p0) REVERT: D 73 MET cc_start: 0.8300 (mmt) cc_final: 0.8099 (mmt) REVERT: D 163 ILE cc_start: 0.8972 (pt) cc_final: 0.8446 (mt) REVERT: D 164 MET cc_start: 0.7761 (mpp) cc_final: 0.7501 (mpp) REVERT: D 181 GLU cc_start: 0.8876 (pt0) cc_final: 0.8631 (pp20) REVERT: D 200 TYR cc_start: 0.8375 (m-80) cc_final: 0.8058 (m-80) REVERT: D 288 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8010 (tm-30) REVERT: D 326 VAL cc_start: 0.8944 (t) cc_final: 0.8727 (t) REVERT: D 379 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8710 (mtmm) REVERT: I 19 LYS cc_start: 0.8681 (mmtp) cc_final: 0.8155 (mtpt) REVERT: I 149 THR cc_start: 0.9254 (p) cc_final: 0.8950 (p) REVERT: I 163 ILE cc_start: 0.8845 (pt) cc_final: 0.8463 (tp) REVERT: I 164 MET cc_start: 0.7829 (mpp) cc_final: 0.7479 (mpp) REVERT: I 200 TYR cc_start: 0.8271 (m-80) cc_final: 0.7860 (m-80) REVERT: I 242 PHE cc_start: 0.7924 (m-80) cc_final: 0.7573 (m-10) REVERT: I 257 MET cc_start: 0.8550 (mtm) cc_final: 0.8330 (mtp) REVERT: I 297 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8020 (mmtt) REVERT: I 321 MET cc_start: 0.8529 (pmm) cc_final: 0.8322 (pmm) REVERT: I 328 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8534 (mm-30) REVERT: I 363 MET cc_start: 0.8111 (ptp) cc_final: 0.7750 (ptm) REVERT: I 425 TYR cc_start: 0.8492 (m-80) cc_final: 0.8096 (m-80) REVERT: H 118 ASP cc_start: 0.8473 (m-30) cc_final: 0.8181 (m-30) REVERT: H 163 ILE cc_start: 0.8840 (pt) cc_final: 0.8408 (mt) REVERT: H 250 LEU cc_start: 0.8278 (mm) cc_final: 0.7683 (mp) REVERT: H 267 MET cc_start: 0.7171 (mtm) cc_final: 0.6835 (mtm) REVERT: H 291 GLN cc_start: 0.7944 (mm110) cc_final: 0.7693 (mm110) REVERT: H 297 LYS cc_start: 0.8720 (ptpt) cc_final: 0.8432 (mmtm) REVERT: H 363 MET cc_start: 0.8254 (mtp) cc_final: 0.7986 (mtp) outliers start: 5 outliers final: 0 residues processed: 976 average time/residue: 0.2456 time to fit residues: 396.5359 Evaluate side-chains 645 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 644 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 81 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 345 optimal weight: 40.0000 chunk 167 optimal weight: 9.9990 chunk 462 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 330 optimal weight: 30.0000 chunk 454 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 overall best weight: 9.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN E 380 ASN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 HIS K 380 ASN B 291 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 337 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN G 337 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN I 292 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.081823 restraints weight = 127956.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084375 restraints weight = 74233.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.086151 restraints weight = 47766.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.087452 restraints weight = 33005.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.088357 restraints weight = 23981.567| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 41454 Z= 0.220 Angle : 0.649 8.859 56328 Z= 0.344 Chirality : 0.046 0.163 6162 Planarity : 0.005 0.064 7326 Dihedral : 11.968 179.810 5658 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.07 % Allowed : 3.21 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.11), residues: 5064 helix: -1.25 (0.10), residues: 2178 sheet: -0.92 (0.19), residues: 708 loop : -1.96 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 422 TYR 0.029 0.002 TYR C 24 PHE 0.021 0.002 PHE K 255 TRP 0.048 0.003 TRP D 397 HIS 0.010 0.002 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (41454) covalent geometry : angle 0.64869 / 0.34 (56328) hydrogen bonds : bond 0.04676 / 3.11 ( 1411) hydrogen bonds : angle 5.53311 / 3.89 ( 4107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 881 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.6971 (ptm) cc_final: 0.5933 (tmm) REVERT: E 54 SER cc_start: 0.7572 (p) cc_final: 0.7131 (t) REVERT: E 205 ASP cc_start: 0.7567 (t0) cc_final: 0.6342 (m-30) REVERT: E 211 ASP cc_start: 0.6873 (t0) cc_final: 0.6184 (p0) REVERT: E 213 CYS cc_start: 0.8476 (t) cc_final: 0.8187 (t) REVERT: E 221 ARG cc_start: 0.8391 (mtt90) cc_final: 0.8183 (mpp-170) REVERT: E 267 PHE cc_start: 0.9065 (m-80) cc_final: 0.8837 (m-80) REVERT: E 293 ASN cc_start: 0.8843 (m110) cc_final: 0.8597 (m110) REVERT: E 313 MET cc_start: 0.7979 (mtm) cc_final: 0.6757 (mtp) REVERT: E 351 PHE cc_start: 0.7953 (m-80) cc_final: 0.7471 (m-80) REVERT: J 14 VAL cc_start: 0.9274 (t) cc_final: 0.9042 (p) REVERT: J 16 ILE cc_start: 0.9475 (mt) cc_final: 0.9070 (mm) REVERT: J 124 LYS cc_start: 0.8405 (mttm) cc_final: 0.8104 (tptp) REVERT: J 205 ASP cc_start: 0.7520 (t0) cc_final: 0.6610 (m-30) REVERT: J 214 ARG cc_start: 0.8194 (ptm160) cc_final: 0.7770 (ptm-80) REVERT: J 260 VAL cc_start: 0.8748 (t) cc_final: 0.8370 (p) REVERT: J 267 PHE cc_start: 0.9060 (m-80) cc_final: 0.8812 (m-80) REVERT: J 313 MET cc_start: 0.7699 (mtm) cc_final: 0.6385 (mtp) REVERT: J 351 PHE cc_start: 0.7750 (m-80) cc_final: 0.7512 (m-80) REVERT: C 36 MET cc_start: 0.6783 (ptm) cc_final: 0.5957 (tmm) REVERT: C 149 PHE cc_start: 0.8060 (t80) cc_final: 0.7730 (t80) REVERT: C 205 ASP cc_start: 0.7561 (t0) cc_final: 0.6969 (m-30) REVERT: C 301 GLN cc_start: 0.8747 (mt0) cc_final: 0.8170 (pt0) REVERT: C 313 MET cc_start: 0.7713 (mtm) cc_final: 0.6660 (mtp) REVERT: C 377 MET cc_start: 0.7710 (ttp) cc_final: 0.6911 (tmm) REVERT: L 36 MET cc_start: 0.7162 (ptm) cc_final: 0.6176 (tmm) REVERT: L 195 LEU cc_start: 0.7944 (mm) cc_final: 0.7610 (mm) REVERT: L 205 ASP cc_start: 0.7635 (t0) cc_final: 0.6755 (m-30) REVERT: L 301 GLN cc_start: 0.8661 (mt0) cc_final: 0.8380 (pt0) REVERT: L 302 MET cc_start: 0.8960 (mmm) cc_final: 0.8751 (mmm) REVERT: L 313 MET cc_start: 0.7327 (mtm) cc_final: 0.5960 (mtp) REVERT: A 36 MET cc_start: 0.6625 (ptm) cc_final: 0.6408 (tmm) REVERT: A 119 LEU cc_start: 0.9220 (mt) cc_final: 0.8970 (mm) REVERT: A 205 ASP cc_start: 0.7435 (t0) cc_final: 0.6374 (m-30) REVERT: A 255 PHE cc_start: 0.7214 (m-80) cc_final: 0.6887 (m-80) REVERT: A 267 PHE cc_start: 0.8945 (m-80) cc_final: 0.8553 (m-80) REVERT: A 413 MET cc_start: 0.7899 (tpp) cc_final: 0.7417 (mmm) REVERT: K 54 SER cc_start: 0.7107 (p) cc_final: 0.6644 (t) REVERT: K 149 PHE cc_start: 0.8282 (t80) cc_final: 0.8029 (t80) REVERT: K 205 ASP cc_start: 0.7184 (t0) cc_final: 0.6124 (m-30) REVERT: K 267 PHE cc_start: 0.8927 (m-80) cc_final: 0.8551 (m-80) REVERT: K 302 MET cc_start: 0.8763 (mmm) cc_final: 0.8394 (mmm) REVERT: B 51 TYR cc_start: 0.8094 (m-80) cc_final: 0.7348 (m-10) REVERT: B 181 GLU cc_start: 0.8881 (pt0) cc_final: 0.8427 (pp20) REVERT: B 270 PHE cc_start: 0.8345 (t80) cc_final: 0.8112 (t80) REVERT: B 297 LYS cc_start: 0.8795 (ptpt) cc_final: 0.8487 (mtmm) REVERT: F 51 TYR cc_start: 0.7959 (m-80) cc_final: 0.7032 (m-10) REVERT: F 85 PHE cc_start: 0.8195 (m-80) cc_final: 0.7705 (m-80) REVERT: F 163 ILE cc_start: 0.8749 (pt) cc_final: 0.8335 (mt) REVERT: F 197 ASP cc_start: 0.8033 (m-30) cc_final: 0.7824 (t70) REVERT: F 216 LYS cc_start: 0.8243 (mmtp) cc_final: 0.7915 (mmtm) REVERT: F 233 MET cc_start: 0.9282 (mtp) cc_final: 0.8814 (mtm) REVERT: F 267 MET cc_start: 0.7552 (mtm) cc_final: 0.7190 (mtm) REVERT: F 379 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8050 (pttp) REVERT: G 6 HIS cc_start: 0.8907 (t70) cc_final: 0.8561 (t70) REVERT: G 83 GLN cc_start: 0.8521 (mp10) cc_final: 0.7946 (mm110) REVERT: G 164 MET cc_start: 0.8143 (mpp) cc_final: 0.7936 (mpp) REVERT: G 233 MET cc_start: 0.9167 (mtp) cc_final: 0.8745 (mtm) REVERT: G 267 MET cc_start: 0.7438 (mtm) cc_final: 0.7196 (mtm) REVERT: G 321 MET cc_start: 0.8456 (ptp) cc_final: 0.7392 (ptp) REVERT: G 323 MET cc_start: 0.7705 (mpp) cc_final: 0.7351 (mmt) REVERT: D 163 ILE cc_start: 0.9119 (pt) cc_final: 0.8660 (mt) REVERT: D 181 GLU cc_start: 0.8701 (pt0) cc_final: 0.8469 (pp20) REVERT: D 200 TYR cc_start: 0.8397 (m-80) cc_final: 0.8087 (m-80) REVERT: D 288 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 299 MET cc_start: 0.9325 (mmp) cc_final: 0.8725 (mmm) REVERT: D 379 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8659 (mtmm) REVERT: D 388 MET cc_start: 0.7224 (mtt) cc_final: 0.6835 (mtt) REVERT: I 22 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7026 (tm-30) REVERT: I 23 VAL cc_start: 0.7911 (t) cc_final: 0.7144 (t) REVERT: I 90 PHE cc_start: 0.7731 (m-80) cc_final: 0.7516 (m-80) REVERT: I 149 THR cc_start: 0.9238 (p) cc_final: 0.8937 (p) REVERT: I 242 PHE cc_start: 0.7831 (m-80) cc_final: 0.7478 (m-10) REVERT: I 257 MET cc_start: 0.8543 (mtm) cc_final: 0.8126 (mtp) REVERT: I 297 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8100 (mmtt) REVERT: H 163 ILE cc_start: 0.8744 (pt) cc_final: 0.8501 (tt) REVERT: H 233 MET cc_start: 0.8880 (mtm) cc_final: 0.8680 (mtm) REVERT: H 266 PHE cc_start: 0.8511 (m-10) cc_final: 0.8250 (m-10) REVERT: H 297 LYS cc_start: 0.8697 (ptpt) cc_final: 0.8424 (mmtm) REVERT: H 395 LEU cc_start: 0.7253 (tp) cc_final: 0.7034 (tp) outliers start: 3 outliers final: 2 residues processed: 883 average time/residue: 0.2450 time to fit residues: 358.8453 Evaluate side-chains 613 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 611 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 185 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 chunk 497 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 319 optimal weight: 6.9990 chunk 370 optimal weight: 30.0000 chunk 433 optimal weight: 5.9990 chunk 327 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 380 ASN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 291 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN G 291 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN I 291 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN H 292 GLN H 298 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.093341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.082725 restraints weight = 126308.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.085339 restraints weight = 72665.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087181 restraints weight = 46365.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.088495 restraints weight = 31785.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.089397 restraints weight = 22921.432| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 41454 Z= 0.150 Angle : 0.581 8.873 56328 Z= 0.303 Chirality : 0.045 0.207 6162 Planarity : 0.004 0.049 7326 Dihedral : 11.830 179.252 5658 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.21 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.11), residues: 5064 helix: -0.94 (0.10), residues: 2196 sheet: -0.80 (0.19), residues: 720 loop : -1.77 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 339 TYR 0.027 0.002 TYR L 24 PHE 0.031 0.001 PHE H 81 TRP 0.033 0.002 TRP D 397 HIS 0.009 0.001 HIS H 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (41454) covalent geometry : angle 0.58083 / 0.30 (56328) hydrogen bonds : bond 0.04032 / 2.69 ( 1411) hydrogen bonds : angle 5.16431 / 3.61 ( 4107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 888 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7093 (ptm) cc_final: 0.5960 (tmm) REVERT: E 54 SER cc_start: 0.7250 (p) cc_final: 0.6983 (t) REVERT: E 149 PHE cc_start: 0.8321 (t80) cc_final: 0.8018 (t80) REVERT: E 205 ASP cc_start: 0.7303 (t0) cc_final: 0.6496 (m-30) REVERT: E 211 ASP cc_start: 0.6890 (t0) cc_final: 0.6068 (p0) REVERT: E 213 CYS cc_start: 0.8608 (t) cc_final: 0.8243 (t) REVERT: E 250 VAL cc_start: 0.7896 (t) cc_final: 0.7594 (t) REVERT: E 267 PHE cc_start: 0.9117 (m-80) cc_final: 0.8773 (m-80) REVERT: E 293 ASN cc_start: 0.8877 (m110) cc_final: 0.8539 (m110) REVERT: E 313 MET cc_start: 0.8014 (mtm) cc_final: 0.6837 (mtp) REVERT: E 326 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8147 (pttt) REVERT: E 351 PHE cc_start: 0.7868 (m-80) cc_final: 0.7368 (m-80) REVERT: E 425 MET cc_start: 0.8958 (tpt) cc_final: 0.8599 (tpp) REVERT: J 14 VAL cc_start: 0.9323 (t) cc_final: 0.8925 (p) REVERT: J 16 ILE cc_start: 0.9449 (mt) cc_final: 0.8947 (mm) REVERT: J 124 LYS cc_start: 0.8430 (mttm) cc_final: 0.8118 (tptp) REVERT: J 149 PHE cc_start: 0.8522 (t80) cc_final: 0.8305 (t80) REVERT: J 205 ASP cc_start: 0.7498 (t0) cc_final: 0.6651 (m-30) REVERT: J 260 VAL cc_start: 0.8751 (t) cc_final: 0.8299 (p) REVERT: J 267 PHE cc_start: 0.9106 (m-80) cc_final: 0.8807 (m-80) REVERT: J 313 MET cc_start: 0.7666 (mtm) cc_final: 0.6533 (ttt) REVERT: J 351 PHE cc_start: 0.7665 (m-80) cc_final: 0.7427 (m-80) REVERT: C 36 MET cc_start: 0.6965 (ptm) cc_final: 0.5935 (tmm) REVERT: C 149 PHE cc_start: 0.8068 (t80) cc_final: 0.7815 (t80) REVERT: C 205 ASP cc_start: 0.7486 (t0) cc_final: 0.6930 (m-30) REVERT: C 257 THR cc_start: 0.9066 (m) cc_final: 0.8693 (p) REVERT: C 301 GLN cc_start: 0.8779 (mt0) cc_final: 0.8112 (pt0) REVERT: C 313 MET cc_start: 0.7768 (mtm) cc_final: 0.6610 (mtp) REVERT: C 377 MET cc_start: 0.7785 (ttp) cc_final: 0.6875 (tmm) REVERT: C 420 GLU cc_start: 0.7959 (tt0) cc_final: 0.7606 (tp30) REVERT: L 36 MET cc_start: 0.7319 (ptm) cc_final: 0.6183 (tmm) REVERT: L 149 PHE cc_start: 0.8345 (t80) cc_final: 0.8009 (t80) REVERT: L 195 LEU cc_start: 0.8053 (mm) cc_final: 0.7713 (mm) REVERT: L 205 ASP cc_start: 0.7575 (t0) cc_final: 0.6794 (m-30) REVERT: L 301 GLN cc_start: 0.8777 (mt0) cc_final: 0.8427 (pt0) REVERT: L 302 MET cc_start: 0.9167 (mmt) cc_final: 0.8935 (mmm) REVERT: L 313 MET cc_start: 0.7420 (mtm) cc_final: 0.6107 (mtp) REVERT: A 36 MET cc_start: 0.6762 (ptm) cc_final: 0.5743 (tmm) REVERT: A 119 LEU cc_start: 0.9262 (mt) cc_final: 0.9061 (mm) REVERT: A 205 ASP cc_start: 0.7340 (t0) cc_final: 0.6224 (m-30) REVERT: A 255 PHE cc_start: 0.7128 (m-80) cc_final: 0.6904 (m-80) REVERT: A 377 MET cc_start: 0.7895 (ttp) cc_final: 0.7382 (ttp) REVERT: A 413 MET cc_start: 0.7840 (tpp) cc_final: 0.7343 (mmm) REVERT: A 420 GLU cc_start: 0.7853 (tt0) cc_final: 0.7456 (tp30) REVERT: K 54 SER cc_start: 0.7307 (p) cc_final: 0.6804 (t) REVERT: K 149 PHE cc_start: 0.8364 (t80) cc_final: 0.8061 (t80) REVERT: K 205 ASP cc_start: 0.6990 (t0) cc_final: 0.6262 (m-30) REVERT: K 267 PHE cc_start: 0.9025 (m-80) cc_final: 0.8663 (m-80) REVERT: K 315 CYS cc_start: 0.9106 (t) cc_final: 0.8732 (t) REVERT: K 377 MET cc_start: 0.8073 (ttt) cc_final: 0.7140 (tmm) REVERT: B 6 HIS cc_start: 0.8918 (t70) cc_final: 0.8225 (t-170) REVERT: B 21 TRP cc_start: 0.8930 (m100) cc_final: 0.7984 (m100) REVERT: B 51 TYR cc_start: 0.8142 (m-80) cc_final: 0.7248 (m-10) REVERT: B 181 GLU cc_start: 0.8864 (pt0) cc_final: 0.8374 (pp20) REVERT: B 257 MET cc_start: 0.8598 (mtt) cc_final: 0.8308 (mtp) REVERT: B 297 LYS cc_start: 0.8763 (ptpt) cc_final: 0.8420 (mtmm) REVERT: F 85 PHE cc_start: 0.8181 (m-80) cc_final: 0.7694 (m-80) REVERT: F 90 PHE cc_start: 0.8323 (m-80) cc_final: 0.8117 (m-80) REVERT: F 163 ILE cc_start: 0.8757 (pt) cc_final: 0.8471 (mp) REVERT: F 197 ASP cc_start: 0.7988 (m-30) cc_final: 0.7591 (t70) REVERT: F 198 GLU cc_start: 0.8057 (pt0) cc_final: 0.7819 (pt0) REVERT: F 216 LYS cc_start: 0.8451 (mmtp) cc_final: 0.8038 (mmtm) REVERT: F 233 MET cc_start: 0.9264 (mtp) cc_final: 0.8912 (mtm) REVERT: F 267 MET cc_start: 0.7477 (mtm) cc_final: 0.7247 (mtm) REVERT: F 406 MET cc_start: 0.8250 (mmm) cc_final: 0.8046 (tpt) REVERT: G 6 HIS cc_start: 0.8871 (t70) cc_final: 0.8601 (t70) REVERT: G 83 GLN cc_start: 0.8190 (mp10) cc_final: 0.7606 (pp30) REVERT: G 164 MET cc_start: 0.8288 (mpp) cc_final: 0.8002 (mpp) REVERT: G 180 VAL cc_start: 0.8783 (m) cc_final: 0.8458 (p) REVERT: G 233 MET cc_start: 0.9107 (mtp) cc_final: 0.8772 (mtm) REVERT: G 245 GLN cc_start: 0.7997 (mm110) cc_final: 0.7789 (mm-40) REVERT: G 257 MET cc_start: 0.8780 (mtm) cc_final: 0.8534 (mtt) REVERT: G 321 MET cc_start: 0.8240 (ptp) cc_final: 0.7697 (ptp) REVERT: D 22 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8416 (mm-30) REVERT: D 58 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7569 (mtpp) REVERT: D 181 GLU cc_start: 0.8729 (pt0) cc_final: 0.8481 (pp20) REVERT: D 245 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7453 (mm-40) REVERT: D 257 MET cc_start: 0.9034 (mtm) cc_final: 0.8544 (mtp) REVERT: D 299 MET cc_start: 0.9333 (mmp) cc_final: 0.8762 (mmm) REVERT: D 323 MET cc_start: 0.7414 (mpp) cc_final: 0.6856 (mpp) REVERT: D 388 MET cc_start: 0.7387 (mtt) cc_final: 0.7040 (mtt) REVERT: D 425 TYR cc_start: 0.8380 (m-80) cc_final: 0.7780 (m-10) REVERT: I 118 ASP cc_start: 0.8434 (m-30) cc_final: 0.8019 (t70) REVERT: I 149 THR cc_start: 0.9421 (p) cc_final: 0.9053 (p) REVERT: I 200 TYR cc_start: 0.8257 (m-80) cc_final: 0.7926 (m-80) REVERT: I 242 PHE cc_start: 0.7841 (m-80) cc_final: 0.7430 (m-10) REVERT: I 297 LYS cc_start: 0.8528 (ptpt) cc_final: 0.8091 (mmtt) REVERT: I 299 MET cc_start: 0.9263 (mmp) cc_final: 0.8780 (mmm) REVERT: I 362 LYS cc_start: 0.9189 (tptt) cc_final: 0.8451 (tppt) REVERT: H 23 VAL cc_start: 0.8340 (t) cc_final: 0.8128 (t) REVERT: H 267 MET cc_start: 0.7108 (mtm) cc_final: 0.6904 (mtm) REVERT: H 297 LYS cc_start: 0.8646 (ptpt) cc_final: 0.8387 (mmtm) REVERT: H 321 MET cc_start: 0.8806 (pmm) cc_final: 0.8519 (pmm) REVERT: H 395 LEU cc_start: 0.7164 (tp) cc_final: 0.6957 (tp) outliers start: 0 outliers final: 0 residues processed: 888 average time/residue: 0.2430 time to fit residues: 361.4591 Evaluate side-chains 615 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 113 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 482 optimal weight: 20.0000 chunk 463 optimal weight: 6.9990 chunk 329 optimal weight: 0.0040 chunk 86 optimal weight: 7.9990 chunk 198 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 overall best weight: 3.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 ASN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 ASN L 11 GLN ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 283 HIS A 372 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 291 GLN B 292 GLN B 298 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN D 347 ASN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN H 298 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.094337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.083509 restraints weight = 125672.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.086175 restraints weight = 72480.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.088041 restraints weight = 46334.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.089372 restraints weight = 31803.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.090317 restraints weight = 22959.165| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41454 Z= 0.117 Angle : 0.545 8.353 56328 Z= 0.281 Chirality : 0.044 0.161 6162 Planarity : 0.004 0.057 7326 Dihedral : 11.616 178.765 5658 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.11), residues: 5064 helix: -0.53 (0.11), residues: 2190 sheet: -0.45 (0.19), residues: 750 loop : -1.63 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 79 TYR 0.028 0.001 TYR L 24 PHE 0.017 0.001 PHE K 351 TRP 0.025 0.002 TRP D 397 HIS 0.010 0.001 HIS H 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (41454) covalent geometry : angle 0.54515 / 0.28 (56328) hydrogen bonds : bond 0.03544 / 2.37 ( 1411) hydrogen bonds : angle 4.77927 / 3.35 ( 4107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 886 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7116 (ptm) cc_final: 0.6076 (tmm) REVERT: E 54 SER cc_start: 0.7212 (p) cc_final: 0.6928 (t) REVERT: E 135 PHE cc_start: 0.8374 (m-80) cc_final: 0.8015 (m-10) REVERT: E 149 PHE cc_start: 0.8316 (t80) cc_final: 0.7988 (t80) REVERT: E 205 ASP cc_start: 0.7257 (t0) cc_final: 0.6350 (m-30) REVERT: E 211 ASP cc_start: 0.6862 (t0) cc_final: 0.6435 (p0) REVERT: E 213 CYS cc_start: 0.8605 (t) cc_final: 0.8224 (t) REVERT: E 267 PHE cc_start: 0.9062 (m-80) cc_final: 0.8747 (m-80) REVERT: E 293 ASN cc_start: 0.8879 (m110) cc_final: 0.8353 (m110) REVERT: E 301 GLN cc_start: 0.8571 (mt0) cc_final: 0.8234 (mt0) REVERT: E 302 MET cc_start: 0.8061 (mtt) cc_final: 0.7852 (mtt) REVERT: E 313 MET cc_start: 0.8053 (mtm) cc_final: 0.6954 (mtp) REVERT: E 326 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8195 (pttt) REVERT: E 351 PHE cc_start: 0.7780 (m-80) cc_final: 0.7359 (m-80) REVERT: J 14 VAL cc_start: 0.9344 (t) cc_final: 0.9104 (p) REVERT: J 16 ILE cc_start: 0.9431 (mt) cc_final: 0.8973 (mm) REVERT: J 124 LYS cc_start: 0.8347 (mttm) cc_final: 0.8137 (tptp) REVERT: J 203 MET cc_start: 0.8651 (mmp) cc_final: 0.8399 (ttp) REVERT: J 205 ASP cc_start: 0.7654 (t0) cc_final: 0.6768 (m-30) REVERT: J 260 VAL cc_start: 0.8626 (t) cc_final: 0.8124 (p) REVERT: J 267 PHE cc_start: 0.9093 (m-80) cc_final: 0.8775 (m-80) REVERT: J 313 MET cc_start: 0.7703 (mtm) cc_final: 0.6635 (ttt) REVERT: C 36 MET cc_start: 0.7169 (ptm) cc_final: 0.6008 (tmm) REVERT: C 205 ASP cc_start: 0.7361 (t0) cc_final: 0.6754 (m-30) REVERT: C 257 THR cc_start: 0.8966 (m) cc_final: 0.8553 (p) REVERT: C 301 GLN cc_start: 0.8818 (mt0) cc_final: 0.8014 (pm20) REVERT: C 313 MET cc_start: 0.7693 (mtm) cc_final: 0.6602 (mtp) REVERT: C 377 MET cc_start: 0.7882 (ttp) cc_final: 0.6886 (tmm) REVERT: C 420 GLU cc_start: 0.7974 (tt0) cc_final: 0.7580 (tp30) REVERT: L 36 MET cc_start: 0.7411 (ptm) cc_final: 0.6176 (tmm) REVERT: L 136 LEU cc_start: 0.8994 (mt) cc_final: 0.8777 (mt) REVERT: L 205 ASP cc_start: 0.7527 (t0) cc_final: 0.6796 (m-30) REVERT: L 301 GLN cc_start: 0.8697 (mt0) cc_final: 0.8159 (pm20) REVERT: L 302 MET cc_start: 0.9148 (mmt) cc_final: 0.8869 (mmm) REVERT: L 313 MET cc_start: 0.7379 (mtm) cc_final: 0.6509 (mtp) REVERT: L 395 PHE cc_start: 0.8984 (t80) cc_final: 0.8714 (t80) REVERT: A 36 MET cc_start: 0.6779 (ptm) cc_final: 0.5720 (tmm) REVERT: A 88 HIS cc_start: 0.8352 (t-90) cc_final: 0.7800 (t-90) REVERT: A 194 THR cc_start: 0.9026 (t) cc_final: 0.8793 (t) REVERT: A 195 LEU cc_start: 0.7972 (mm) cc_final: 0.7555 (mm) REVERT: A 205 ASP cc_start: 0.7594 (t0) cc_final: 0.6291 (m-30) REVERT: A 237 SER cc_start: 0.9157 (m) cc_final: 0.8171 (t) REVERT: A 316 CYS cc_start: 0.8650 (t) cc_final: 0.8264 (t) REVERT: A 377 MET cc_start: 0.8210 (ttp) cc_final: 0.7961 (ttp) REVERT: A 413 MET cc_start: 0.7944 (tpp) cc_final: 0.7479 (mmm) REVERT: A 420 GLU cc_start: 0.8005 (tt0) cc_final: 0.7572 (tp30) REVERT: K 54 SER cc_start: 0.7459 (p) cc_final: 0.6941 (t) REVERT: K 149 PHE cc_start: 0.8378 (t80) cc_final: 0.8113 (t80) REVERT: K 205 ASP cc_start: 0.7021 (t0) cc_final: 0.6239 (m-30) REVERT: K 255 PHE cc_start: 0.7346 (m-80) cc_final: 0.6755 (m-80) REVERT: K 267 PHE cc_start: 0.9034 (m-80) cc_final: 0.8601 (m-80) REVERT: K 315 CYS cc_start: 0.9048 (t) cc_final: 0.8359 (t) REVERT: K 377 MET cc_start: 0.7571 (ttt) cc_final: 0.7342 (tmm) REVERT: B 6 HIS cc_start: 0.8741 (t70) cc_final: 0.8387 (t-170) REVERT: B 21 TRP cc_start: 0.8934 (m100) cc_final: 0.8065 (m100) REVERT: B 51 TYR cc_start: 0.8119 (m-80) cc_final: 0.7241 (m-10) REVERT: B 83 GLN cc_start: 0.8357 (mp10) cc_final: 0.8114 (pp30) REVERT: B 147 MET cc_start: 0.8249 (tmm) cc_final: 0.8035 (tmm) REVERT: B 181 GLU cc_start: 0.8938 (pt0) cc_final: 0.8398 (pp20) REVERT: B 297 LYS cc_start: 0.8767 (ptpt) cc_final: 0.8453 (mtmm) REVERT: B 363 MET cc_start: 0.8419 (mtm) cc_final: 0.8080 (mtm) REVERT: F 51 TYR cc_start: 0.7590 (m-80) cc_final: 0.6970 (m-10) REVERT: F 85 PHE cc_start: 0.8242 (m-80) cc_final: 0.7872 (m-80) REVERT: F 164 MET cc_start: 0.8068 (mpp) cc_final: 0.7690 (mpp) REVERT: F 216 LYS cc_start: 0.8445 (mmtp) cc_final: 0.7998 (mmtm) REVERT: F 233 MET cc_start: 0.9180 (mtp) cc_final: 0.8882 (mtm) REVERT: G 58 LYS cc_start: 0.6933 (mtpp) cc_final: 0.6518 (mtmt) REVERT: G 83 GLN cc_start: 0.8215 (mp10) cc_final: 0.7686 (mm110) REVERT: G 164 MET cc_start: 0.8224 (mpp) cc_final: 0.7724 (mpp) REVERT: G 180 VAL cc_start: 0.8718 (m) cc_final: 0.8400 (p) REVERT: G 216 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7912 (mmtm) REVERT: G 233 MET cc_start: 0.9027 (mtp) cc_final: 0.8627 (mtm) REVERT: G 321 MET cc_start: 0.8292 (ptp) cc_final: 0.7717 (ptp) REVERT: D 21 TRP cc_start: 0.8975 (m100) cc_final: 0.8434 (m100) REVERT: D 22 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8467 (mm-30) REVERT: D 58 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7551 (mtpp) REVERT: D 163 ILE cc_start: 0.9100 (pt) cc_final: 0.8648 (mp) REVERT: D 181 GLU cc_start: 0.8635 (pt0) cc_final: 0.8370 (pp20) REVERT: D 257 MET cc_start: 0.8981 (mtm) cc_final: 0.8535 (mtp) REVERT: D 299 MET cc_start: 0.9315 (mmp) cc_final: 0.8725 (mmm) REVERT: D 312 THR cc_start: 0.7929 (t) cc_final: 0.7407 (p) REVERT: D 347 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8490 (t0) REVERT: D 388 MET cc_start: 0.7460 (mtt) cc_final: 0.7178 (mtt) REVERT: D 425 TYR cc_start: 0.8395 (m-80) cc_final: 0.7970 (m-10) REVERT: I 22 GLU cc_start: 0.7643 (tm-30) cc_final: 0.6979 (tm-30) REVERT: I 23 VAL cc_start: 0.7946 (t) cc_final: 0.7079 (t) REVERT: I 118 ASP cc_start: 0.8404 (m-30) cc_final: 0.7968 (t70) REVERT: I 164 MET cc_start: 0.7847 (mpp) cc_final: 0.7577 (mpp) REVERT: I 200 TYR cc_start: 0.8197 (m-80) cc_final: 0.7754 (m-80) REVERT: I 242 PHE cc_start: 0.7712 (m-80) cc_final: 0.7382 (m-10) REVERT: I 297 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8039 (mptt) REVERT: I 299 MET cc_start: 0.9301 (mmp) cc_final: 0.8663 (mmm) REVERT: I 328 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8501 (mm-30) REVERT: I 362 LYS cc_start: 0.9145 (tptt) cc_final: 0.8356 (tppt) REVERT: H 22 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8443 (mm-30) REVERT: H 23 VAL cc_start: 0.8403 (t) cc_final: 0.8059 (t) REVERT: H 158 GLU cc_start: 0.7597 (pt0) cc_final: 0.7298 (pt0) REVERT: H 199 THR cc_start: 0.8768 (p) cc_final: 0.8559 (p) REVERT: H 266 PHE cc_start: 0.8381 (m-80) cc_final: 0.7896 (m-80) REVERT: H 293 MET cc_start: 0.7815 (mtp) cc_final: 0.7409 (ptp) REVERT: H 297 LYS cc_start: 0.8591 (ptpt) cc_final: 0.8344 (mmtm) REVERT: H 321 MET cc_start: 0.8663 (pmm) cc_final: 0.8339 (pmm) REVERT: H 425 TYR cc_start: 0.8409 (m-10) cc_final: 0.8047 (m-10) outliers start: 2 outliers final: 0 residues processed: 888 average time/residue: 0.2398 time to fit residues: 359.8920 Evaluate side-chains 639 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 638 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 315 optimal weight: 30.0000 chunk 184 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 489 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 171 optimal weight: 6.9990 chunk 437 optimal weight: 0.1980 chunk 68 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 242 optimal weight: 0.8980 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 ASN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 ASN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS B 245 GLN B 291 GLN B 298 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN G 291 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN H 298 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.094460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.083821 restraints weight = 125796.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.086451 restraints weight = 72398.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.088289 restraints weight = 46188.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.089621 restraints weight = 31533.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.090561 restraints weight = 22677.518| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41454 Z= 0.117 Angle : 0.545 10.397 56328 Z= 0.279 Chirality : 0.044 0.164 6162 Planarity : 0.004 0.053 7326 Dihedral : 11.531 177.865 5658 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.02 % Allowed : 1.17 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.12), residues: 5064 helix: -0.24 (0.11), residues: 2166 sheet: -0.39 (0.19), residues: 720 loop : -1.49 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 79 TYR 0.028 0.001 TYR E 24 PHE 0.027 0.001 PHE B 242 TRP 0.045 0.002 TRP H 101 HIS 0.007 0.001 HIS D 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (41454) covalent geometry : angle 0.54508 / 0.28 (56328) hydrogen bonds : bond 0.03382 / 2.25 ( 1411) hydrogen bonds : angle 4.64263 / 3.25 ( 4107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 874 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7072 (ptm) cc_final: 0.6030 (tmm) REVERT: E 54 SER cc_start: 0.7266 (p) cc_final: 0.6920 (t) REVERT: E 205 ASP cc_start: 0.7344 (t0) cc_final: 0.6352 (m-30) REVERT: E 211 ASP cc_start: 0.7053 (t0) cc_final: 0.6665 (p0) REVERT: E 250 VAL cc_start: 0.7999 (t) cc_final: 0.7724 (t) REVERT: E 267 PHE cc_start: 0.9080 (m-80) cc_final: 0.8748 (m-80) REVERT: E 293 ASN cc_start: 0.8785 (m110) cc_final: 0.8320 (m110) REVERT: E 313 MET cc_start: 0.8057 (mtm) cc_final: 0.6967 (mtp) REVERT: E 326 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8108 (pttm) REVERT: E 351 PHE cc_start: 0.7754 (m-80) cc_final: 0.7283 (m-80) REVERT: J 14 VAL cc_start: 0.9321 (t) cc_final: 0.9116 (p) REVERT: J 203 MET cc_start: 0.8728 (mmp) cc_final: 0.8384 (ttp) REVERT: J 205 ASP cc_start: 0.7702 (t0) cc_final: 0.6780 (m-30) REVERT: J 260 VAL cc_start: 0.8655 (t) cc_final: 0.8179 (p) REVERT: J 267 PHE cc_start: 0.9097 (m-80) cc_final: 0.8835 (m-80) REVERT: J 313 MET cc_start: 0.7734 (mtm) cc_final: 0.6655 (ttt) REVERT: J 391 LEU cc_start: 0.9277 (tp) cc_final: 0.8848 (tp) REVERT: C 36 MET cc_start: 0.7172 (ptm) cc_final: 0.5998 (tmm) REVERT: C 205 ASP cc_start: 0.7569 (t0) cc_final: 0.6677 (m-30) REVERT: C 256 GLN cc_start: 0.8531 (pt0) cc_final: 0.8144 (pt0) REVERT: C 257 THR cc_start: 0.8984 (m) cc_final: 0.8709 (p) REVERT: C 301 GLN cc_start: 0.8757 (mt0) cc_final: 0.8092 (pt0) REVERT: C 313 MET cc_start: 0.7610 (mtm) cc_final: 0.6563 (mtp) REVERT: C 377 MET cc_start: 0.7915 (ttp) cc_final: 0.6919 (tmm) REVERT: C 413 MET cc_start: 0.7711 (tpt) cc_final: 0.7456 (mmm) REVERT: C 420 GLU cc_start: 0.8027 (tt0) cc_final: 0.7616 (tp30) REVERT: L 36 MET cc_start: 0.7377 (ptm) cc_final: 0.6436 (tmm) REVERT: L 165 SER cc_start: 0.7368 (t) cc_final: 0.6562 (t) REVERT: L 205 ASP cc_start: 0.7486 (t0) cc_final: 0.6748 (m-30) REVERT: L 301 GLN cc_start: 0.8688 (mt0) cc_final: 0.8149 (pm20) REVERT: L 302 MET cc_start: 0.9159 (mmt) cc_final: 0.8876 (mmm) REVERT: L 313 MET cc_start: 0.7403 (mtm) cc_final: 0.6151 (mtp) REVERT: L 377 MET cc_start: 0.7587 (ttp) cc_final: 0.7048 (tmm) REVERT: L 395 PHE cc_start: 0.8986 (t80) cc_final: 0.8703 (t80) REVERT: A 36 MET cc_start: 0.6747 (ptm) cc_final: 0.5712 (tmm) REVERT: A 194 THR cc_start: 0.8987 (t) cc_final: 0.8730 (t) REVERT: A 195 LEU cc_start: 0.7877 (mm) cc_final: 0.7426 (mm) REVERT: A 205 ASP cc_start: 0.7390 (t0) cc_final: 0.6386 (m-30) REVERT: A 255 PHE cc_start: 0.7073 (m-80) cc_final: 0.6860 (m-80) REVERT: A 316 CYS cc_start: 0.8610 (t) cc_final: 0.8166 (t) REVERT: A 377 MET cc_start: 0.8279 (ttp) cc_final: 0.7958 (ttp) REVERT: A 413 MET cc_start: 0.7996 (tpp) cc_final: 0.7515 (mmm) REVERT: A 420 GLU cc_start: 0.8032 (tt0) cc_final: 0.7593 (tp30) REVERT: K 54 SER cc_start: 0.7340 (p) cc_final: 0.6865 (t) REVERT: K 76 ASP cc_start: 0.8965 (m-30) cc_final: 0.8599 (m-30) REVERT: K 149 PHE cc_start: 0.8412 (t80) cc_final: 0.8099 (t80) REVERT: K 205 ASP cc_start: 0.7096 (t0) cc_final: 0.6357 (m-30) REVERT: K 218 ASP cc_start: 0.8452 (m-30) cc_final: 0.7828 (t0) REVERT: K 255 PHE cc_start: 0.7016 (m-80) cc_final: 0.6596 (m-80) REVERT: K 267 PHE cc_start: 0.8997 (m-80) cc_final: 0.8649 (m-80) REVERT: K 315 CYS cc_start: 0.9062 (t) cc_final: 0.8337 (t) REVERT: K 377 MET cc_start: 0.7862 (ttt) cc_final: 0.7222 (tmm) REVERT: B 6 HIS cc_start: 0.8779 (t70) cc_final: 0.8484 (t-170) REVERT: B 21 TRP cc_start: 0.8921 (m100) cc_final: 0.8105 (m100) REVERT: B 51 TYR cc_start: 0.8079 (m-80) cc_final: 0.7200 (m-10) REVERT: B 118 ASP cc_start: 0.8312 (m-30) cc_final: 0.7772 (t70) REVERT: B 181 GLU cc_start: 0.8925 (pt0) cc_final: 0.8388 (pp20) REVERT: B 297 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8304 (mmtm) REVERT: B 298 ASN cc_start: 0.7392 (t0) cc_final: 0.7181 (t0) REVERT: B 299 MET cc_start: 0.9162 (mmm) cc_final: 0.8868 (mmm) REVERT: B 353 VAL cc_start: 0.8793 (t) cc_final: 0.8587 (t) REVERT: B 363 MET cc_start: 0.8349 (mtm) cc_final: 0.8063 (mtm) REVERT: B 379 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8339 (mptt) REVERT: F 51 TYR cc_start: 0.7672 (m-80) cc_final: 0.7100 (m-10) REVERT: F 164 MET cc_start: 0.8100 (mpp) cc_final: 0.7726 (mpp) REVERT: F 216 LYS cc_start: 0.8413 (mmtp) cc_final: 0.7956 (mmtm) REVERT: F 233 MET cc_start: 0.9135 (mtp) cc_final: 0.8845 (mtm) REVERT: F 403 MET cc_start: 0.5646 (mmt) cc_final: 0.5390 (mmt) REVERT: G 6 HIS cc_start: 0.8857 (t70) cc_final: 0.8546 (t70) REVERT: G 58 LYS cc_start: 0.6933 (mtpp) cc_final: 0.6491 (mtmt) REVERT: G 83 GLN cc_start: 0.8246 (mp10) cc_final: 0.7520 (tm-30) REVERT: G 164 MET cc_start: 0.8210 (mpp) cc_final: 0.7782 (mpp) REVERT: G 180 VAL cc_start: 0.8706 (m) cc_final: 0.8450 (p) REVERT: G 216 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7843 (mmtm) REVERT: G 228 LEU cc_start: 0.9155 (mm) cc_final: 0.8782 (tp) REVERT: G 233 MET cc_start: 0.8973 (mtp) cc_final: 0.8645 (mtm) REVERT: G 321 MET cc_start: 0.8247 (ptp) cc_final: 0.7710 (ptp) REVERT: G 332 ASN cc_start: 0.7605 (m-40) cc_final: 0.7230 (p0) REVERT: D 21 TRP cc_start: 0.9038 (m100) cc_final: 0.8428 (m100) REVERT: D 22 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8464 (mm-30) REVERT: D 58 LYS cc_start: 0.7718 (ttmm) cc_final: 0.7488 (mtpp) REVERT: D 163 ILE cc_start: 0.9101 (pt) cc_final: 0.8687 (mp) REVERT: D 181 GLU cc_start: 0.8572 (pt0) cc_final: 0.8344 (pp20) REVERT: D 245 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7732 (mm-40) REVERT: D 257 MET cc_start: 0.8957 (mtm) cc_final: 0.8540 (mtp) REVERT: D 299 MET cc_start: 0.9321 (mmp) cc_final: 0.8784 (mmm) REVERT: D 362 LYS cc_start: 0.9024 (tptt) cc_final: 0.8802 (tptt) REVERT: D 425 TYR cc_start: 0.8390 (m-80) cc_final: 0.8085 (m-10) REVERT: I 22 GLU cc_start: 0.7590 (tm-30) cc_final: 0.6841 (tm-30) REVERT: I 23 VAL cc_start: 0.8103 (t) cc_final: 0.7415 (t) REVERT: I 27 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8122 (mt-10) REVERT: I 118 ASP cc_start: 0.8352 (m-30) cc_final: 0.8047 (t70) REVERT: I 164 MET cc_start: 0.7918 (mpp) cc_final: 0.7605 (mpp) REVERT: I 198 GLU cc_start: 0.8316 (pt0) cc_final: 0.8059 (pt0) REVERT: I 200 TYR cc_start: 0.8253 (m-80) cc_final: 0.7604 (m-80) REVERT: I 242 PHE cc_start: 0.7505 (m-80) cc_final: 0.7208 (m-10) REVERT: I 297 LYS cc_start: 0.8416 (ptpt) cc_final: 0.8036 (mptt) REVERT: I 362 LYS cc_start: 0.9125 (tptt) cc_final: 0.8889 (tptp) REVERT: I 363 MET cc_start: 0.7966 (ptp) cc_final: 0.7468 (ptt) REVERT: H 51 TYR cc_start: 0.7198 (m-80) cc_final: 0.6932 (m-10) REVERT: H 293 MET cc_start: 0.7828 (mtp) cc_final: 0.7357 (ptp) REVERT: H 321 MET cc_start: 0.8750 (pmm) cc_final: 0.8481 (pmm) REVERT: H 353 VAL cc_start: 0.8734 (t) cc_final: 0.8445 (t) REVERT: H 355 ASP cc_start: 0.7966 (m-30) cc_final: 0.7170 (m-30) outliers start: 1 outliers final: 0 residues processed: 875 average time/residue: 0.2356 time to fit residues: 348.3362 Evaluate side-chains 630 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 630 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 85 optimal weight: 9.9990 chunk 409 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 299 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 389 optimal weight: 4.9990 chunk 450 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 ASN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 298 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 337 ASN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 291 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 ASN H 298 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.093045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.082489 restraints weight = 127577.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.085053 restraints weight = 74047.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.086845 restraints weight = 47600.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.088150 restraints weight = 32900.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089030 restraints weight = 23817.672| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41454 Z= 0.154 Angle : 0.579 8.273 56328 Z= 0.300 Chirality : 0.045 0.238 6162 Planarity : 0.004 0.052 7326 Dihedral : 11.552 178.018 5658 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.12), residues: 5064 helix: -0.19 (0.11), residues: 2208 sheet: -0.38 (0.19), residues: 672 loop : -1.53 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 156 TYR 0.017 0.001 TYR E 319 PHE 0.017 0.001 PHE J 351 TRP 0.071 0.003 TRP H 101 HIS 0.007 0.001 HIS H 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (41454) covalent geometry : angle 0.57930 / 0.30 (56328) hydrogen bonds : bond 0.03518 / 2.33 ( 1411) hydrogen bonds : angle 4.77631 / 3.34 ( 4107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 840 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7160 (ptm) cc_final: 0.6116 (tmm) REVERT: E 54 SER cc_start: 0.7445 (p) cc_final: 0.7002 (t) REVERT: E 205 ASP cc_start: 0.7344 (t0) cc_final: 0.6497 (m-30) REVERT: E 267 PHE cc_start: 0.9135 (m-80) cc_final: 0.8763 (m-80) REVERT: E 293 ASN cc_start: 0.8742 (m110) cc_final: 0.8304 (m110) REVERT: E 313 MET cc_start: 0.8052 (mtm) cc_final: 0.6953 (mtp) REVERT: E 326 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8188 (pttm) REVERT: E 351 PHE cc_start: 0.7784 (m-80) cc_final: 0.7294 (m-80) REVERT: J 14 VAL cc_start: 0.9263 (t) cc_final: 0.9042 (p) REVERT: J 203 MET cc_start: 0.8651 (mmp) cc_final: 0.8444 (ttp) REVERT: J 205 ASP cc_start: 0.7697 (t0) cc_final: 0.6898 (m-30) REVERT: J 260 VAL cc_start: 0.8708 (t) cc_final: 0.8196 (p) REVERT: J 267 PHE cc_start: 0.9123 (m-80) cc_final: 0.8856 (m-80) REVERT: J 313 MET cc_start: 0.7689 (mtm) cc_final: 0.6687 (ttt) REVERT: J 352 LYS cc_start: 0.7784 (tptp) cc_final: 0.7506 (mmtt) REVERT: J 377 MET cc_start: 0.8149 (ttt) cc_final: 0.7408 (tmm) REVERT: C 36 MET cc_start: 0.7083 (ptm) cc_final: 0.5821 (tmm) REVERT: C 52 PHE cc_start: 0.8695 (m-10) cc_final: 0.8413 (m-10) REVERT: C 205 ASP cc_start: 0.7599 (t0) cc_final: 0.6883 (m-30) REVERT: C 301 GLN cc_start: 0.8895 (mt0) cc_final: 0.8339 (pt0) REVERT: C 313 MET cc_start: 0.7671 (mtm) cc_final: 0.6535 (mtp) REVERT: C 413 MET cc_start: 0.7778 (tpt) cc_final: 0.7546 (mmm) REVERT: C 420 GLU cc_start: 0.8046 (tt0) cc_final: 0.7638 (tp30) REVERT: L 36 MET cc_start: 0.7625 (ptm) cc_final: 0.6547 (tmm) REVERT: L 52 PHE cc_start: 0.8410 (m-10) cc_final: 0.8087 (m-10) REVERT: L 136 LEU cc_start: 0.8962 (mt) cc_final: 0.8746 (mt) REVERT: L 205 ASP cc_start: 0.7568 (t0) cc_final: 0.6721 (m-30) REVERT: L 260 VAL cc_start: 0.8834 (t) cc_final: 0.8350 (p) REVERT: L 301 GLN cc_start: 0.8721 (mt0) cc_final: 0.8321 (pm20) REVERT: L 302 MET cc_start: 0.9006 (mmt) cc_final: 0.8795 (mmt) REVERT: L 313 MET cc_start: 0.7494 (mtm) cc_final: 0.6200 (mtp) REVERT: A 36 MET cc_start: 0.6593 (ptm) cc_final: 0.5726 (tmm) REVERT: A 55 GLU cc_start: 0.8325 (tt0) cc_final: 0.7859 (pm20) REVERT: A 194 THR cc_start: 0.9056 (t) cc_final: 0.8742 (t) REVERT: A 195 LEU cc_start: 0.7925 (mm) cc_final: 0.7632 (mm) REVERT: A 205 ASP cc_start: 0.7458 (t0) cc_final: 0.6454 (m-30) REVERT: A 255 PHE cc_start: 0.6979 (m-80) cc_final: 0.6767 (m-80) REVERT: A 316 CYS cc_start: 0.8565 (t) cc_final: 0.8050 (t) REVERT: A 351 PHE cc_start: 0.8114 (m-80) cc_final: 0.7483 (m-80) REVERT: A 377 MET cc_start: 0.8266 (ttp) cc_final: 0.7935 (ttp) REVERT: A 413 MET cc_start: 0.8071 (tpp) cc_final: 0.7603 (mmm) REVERT: A 420 GLU cc_start: 0.8117 (tt0) cc_final: 0.7743 (tp30) REVERT: K 54 SER cc_start: 0.7434 (p) cc_final: 0.6969 (t) REVERT: K 149 PHE cc_start: 0.8262 (t80) cc_final: 0.8050 (t80) REVERT: K 203 MET cc_start: 0.8678 (mmp) cc_final: 0.8271 (ttm) REVERT: K 205 ASP cc_start: 0.7020 (t0) cc_final: 0.6112 (m-30) REVERT: K 218 ASP cc_start: 0.8473 (m-30) cc_final: 0.7864 (t0) REVERT: K 267 PHE cc_start: 0.8975 (m-80) cc_final: 0.8606 (m-80) REVERT: K 286 LEU cc_start: 0.8507 (mt) cc_final: 0.8145 (mp) REVERT: K 300 ASN cc_start: 0.8156 (m-40) cc_final: 0.7829 (m-40) REVERT: K 315 CYS cc_start: 0.9187 (t) cc_final: 0.8560 (t) REVERT: K 377 MET cc_start: 0.7785 (ttt) cc_final: 0.7017 (tmm) REVERT: K 420 GLU cc_start: 0.7871 (tt0) cc_final: 0.7623 (tp30) REVERT: B 6 HIS cc_start: 0.8892 (t70) cc_final: 0.8518 (t-170) REVERT: B 21 TRP cc_start: 0.8996 (m100) cc_final: 0.8244 (m100) REVERT: B 181 GLU cc_start: 0.8766 (pt0) cc_final: 0.8252 (pp20) REVERT: B 293 MET cc_start: 0.7147 (pmm) cc_final: 0.6915 (pmm) REVERT: B 297 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8528 (mtmm) REVERT: B 299 MET cc_start: 0.9201 (mmm) cc_final: 0.8902 (mmm) REVERT: B 323 MET cc_start: 0.7032 (mpp) cc_final: 0.6680 (mpp) REVERT: B 328 GLU cc_start: 0.8034 (tp30) cc_final: 0.7755 (tp30) REVERT: B 406 MET cc_start: 0.8589 (mmm) cc_final: 0.8187 (mmt) REVERT: B 415 MET cc_start: 0.8764 (tpt) cc_final: 0.8515 (mmm) REVERT: F 85 PHE cc_start: 0.8361 (m-80) cc_final: 0.7944 (m-80) REVERT: F 90 PHE cc_start: 0.8217 (m-80) cc_final: 0.8009 (m-80) REVERT: F 164 MET cc_start: 0.8114 (mpp) cc_final: 0.7780 (mpp) REVERT: F 216 LYS cc_start: 0.8412 (mmtp) cc_final: 0.7954 (mmtm) REVERT: F 233 MET cc_start: 0.9195 (mtp) cc_final: 0.8938 (mtm) REVERT: F 323 MET cc_start: 0.7520 (mpp) cc_final: 0.7261 (mmt) REVERT: F 403 MET cc_start: 0.5715 (mmt) cc_final: 0.5305 (mmt) REVERT: G 6 HIS cc_start: 0.8932 (t70) cc_final: 0.8566 (t70) REVERT: G 58 LYS cc_start: 0.6972 (mtpp) cc_final: 0.6520 (mtmt) REVERT: G 83 GLN cc_start: 0.8351 (mp10) cc_final: 0.7584 (tm-30) REVERT: G 164 MET cc_start: 0.8291 (mpp) cc_final: 0.7803 (mpp) REVERT: G 180 VAL cc_start: 0.8745 (m) cc_final: 0.8447 (p) REVERT: G 216 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7999 (mmtm) REVERT: G 228 LEU cc_start: 0.9164 (mm) cc_final: 0.8818 (tp) REVERT: G 233 MET cc_start: 0.9017 (mtp) cc_final: 0.8575 (mtm) REVERT: G 321 MET cc_start: 0.8279 (ptp) cc_final: 0.7564 (ptp) REVERT: G 332 ASN cc_start: 0.7574 (m-40) cc_final: 0.7331 (p0) REVERT: D 58 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7495 (mtpp) REVERT: D 149 THR cc_start: 0.9463 (p) cc_final: 0.9202 (p) REVERT: D 163 ILE cc_start: 0.9029 (pt) cc_final: 0.8655 (mp) REVERT: D 181 GLU cc_start: 0.8642 (pt0) cc_final: 0.8404 (pp20) REVERT: D 245 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7773 (mm-40) REVERT: D 299 MET cc_start: 0.9275 (mmp) cc_final: 0.8832 (mmm) REVERT: D 328 GLU cc_start: 0.8459 (tp30) cc_final: 0.8232 (tp30) REVERT: D 362 LYS cc_start: 0.9076 (tptt) cc_final: 0.8825 (tptp) REVERT: D 363 MET cc_start: 0.7929 (ptp) cc_final: 0.7617 (ptt) REVERT: I 22 GLU cc_start: 0.7574 (tm-30) cc_final: 0.6943 (tm-30) REVERT: I 23 VAL cc_start: 0.7804 (t) cc_final: 0.6943 (t) REVERT: I 118 ASP cc_start: 0.8546 (m-30) cc_final: 0.8208 (t70) REVERT: I 149 THR cc_start: 0.9308 (p) cc_final: 0.8961 (p) REVERT: I 164 MET cc_start: 0.7989 (mpp) cc_final: 0.7702 (mpp) REVERT: I 242 PHE cc_start: 0.7535 (m-80) cc_final: 0.7223 (m-10) REVERT: I 293 MET cc_start: 0.7503 (pmm) cc_final: 0.7233 (pmm) REVERT: I 297 LYS cc_start: 0.8386 (ptpt) cc_final: 0.8064 (mptt) REVERT: I 362 LYS cc_start: 0.9115 (tptt) cc_final: 0.8870 (tptp) REVERT: I 363 MET cc_start: 0.8078 (ptp) cc_final: 0.7606 (ptt) REVERT: H 51 TYR cc_start: 0.7156 (m-80) cc_final: 0.6852 (m-10) REVERT: H 293 MET cc_start: 0.7858 (mtp) cc_final: 0.7398 (ptp) REVERT: H 321 MET cc_start: 0.8621 (pmm) cc_final: 0.8398 (pmm) REVERT: H 323 MET cc_start: 0.7037 (mpp) cc_final: 0.6785 (mpp) REVERT: H 353 VAL cc_start: 0.8735 (t) cc_final: 0.8413 (t) REVERT: H 355 ASP cc_start: 0.7896 (m-30) cc_final: 0.7250 (m-30) REVERT: H 406 MET cc_start: 0.8609 (mmm) cc_final: 0.8179 (mmm) outliers start: 0 outliers final: 0 residues processed: 840 average time/residue: 0.2261 time to fit residues: 321.6777 Evaluate side-chains 616 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 616 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 497 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 332 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 465 optimal weight: 30.0000 chunk 415 optimal weight: 5.9990 chunk 491 optimal weight: 5.9990 chunk 326 optimal weight: 30.0000 chunk 408 optimal weight: 7.9990 chunk 445 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 245 GLN B 298 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN G 226 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 291 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.091726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.081215 restraints weight = 130685.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.083757 restraints weight = 75727.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085530 restraints weight = 48670.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.086820 restraints weight = 33684.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.087679 restraints weight = 24499.869| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41454 Z= 0.176 Angle : 0.602 7.979 56328 Z= 0.312 Chirality : 0.046 0.225 6162 Planarity : 0.004 0.053 7326 Dihedral : 11.605 179.442 5658 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.12), residues: 5064 helix: -0.14 (0.11), residues: 2166 sheet: -0.34 (0.19), residues: 690 loop : -1.51 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 156 TYR 0.021 0.002 TYR E 24 PHE 0.023 0.002 PHE H 212 TRP 0.055 0.003 TRP F 101 HIS 0.008 0.002 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (41454) covalent geometry : angle 0.60198 / 0.31 (56328) hydrogen bonds : bond 0.03640 / 2.42 ( 1411) hydrogen bonds : angle 4.96707 / 3.49 ( 4107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 820 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7371 (ptm) cc_final: 0.6114 (tmm) REVERT: E 54 SER cc_start: 0.7454 (p) cc_final: 0.7100 (t) REVERT: E 149 PHE cc_start: 0.8062 (t80) cc_final: 0.7810 (t80) REVERT: E 205 ASP cc_start: 0.7407 (t0) cc_final: 0.6572 (m-30) REVERT: E 250 VAL cc_start: 0.8033 (t) cc_final: 0.7751 (t) REVERT: E 267 PHE cc_start: 0.9176 (m-80) cc_final: 0.8772 (m-80) REVERT: E 293 ASN cc_start: 0.8823 (m110) cc_final: 0.8454 (m110) REVERT: E 313 MET cc_start: 0.8105 (mtm) cc_final: 0.7001 (mtp) REVERT: E 326 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8222 (pttm) REVERT: E 351 PHE cc_start: 0.7809 (m-80) cc_final: 0.7276 (m-80) REVERT: J 205 ASP cc_start: 0.7731 (t0) cc_final: 0.6888 (m-30) REVERT: J 260 VAL cc_start: 0.8687 (t) cc_final: 0.8222 (p) REVERT: J 267 PHE cc_start: 0.9126 (m-80) cc_final: 0.8831 (m-80) REVERT: J 313 MET cc_start: 0.7735 (mtm) cc_final: 0.6717 (ttt) REVERT: J 352 LYS cc_start: 0.7787 (tptp) cc_final: 0.7531 (mmtt) REVERT: J 377 MET cc_start: 0.8118 (ttt) cc_final: 0.7474 (tmm) REVERT: C 36 MET cc_start: 0.7360 (ptm) cc_final: 0.6084 (tmm) REVERT: C 203 MET cc_start: 0.8428 (mmp) cc_final: 0.8167 (mmm) REVERT: C 205 ASP cc_start: 0.7590 (t0) cc_final: 0.6884 (m-30) REVERT: C 301 GLN cc_start: 0.8926 (mt0) cc_final: 0.8305 (pt0) REVERT: C 313 MET cc_start: 0.7770 (mtm) cc_final: 0.6719 (ttt) REVERT: C 413 MET cc_start: 0.7841 (tpt) cc_final: 0.7557 (mmm) REVERT: L 36 MET cc_start: 0.7723 (ptm) cc_final: 0.6459 (tmm) REVERT: L 169 PHE cc_start: 0.8419 (m-80) cc_final: 0.8215 (m-80) REVERT: L 205 ASP cc_start: 0.7582 (t0) cc_final: 0.6776 (m-30) REVERT: L 260 VAL cc_start: 0.8887 (t) cc_final: 0.8371 (p) REVERT: L 301 GLN cc_start: 0.8726 (mt0) cc_final: 0.8444 (pt0) REVERT: L 302 MET cc_start: 0.8980 (mmt) cc_final: 0.8765 (mmt) REVERT: A 24 TYR cc_start: 0.8669 (m-80) cc_final: 0.8385 (m-80) REVERT: A 36 MET cc_start: 0.6707 (ptm) cc_final: 0.5803 (tmm) REVERT: A 55 GLU cc_start: 0.8430 (tt0) cc_final: 0.7893 (pm20) REVERT: A 205 ASP cc_start: 0.7568 (t0) cc_final: 0.6306 (m-30) REVERT: A 255 PHE cc_start: 0.6976 (m-80) cc_final: 0.6762 (m-80) REVERT: A 260 VAL cc_start: 0.9008 (t) cc_final: 0.8625 (p) REVERT: A 316 CYS cc_start: 0.8411 (t) cc_final: 0.7816 (t) REVERT: A 351 PHE cc_start: 0.8189 (m-80) cc_final: 0.7518 (m-80) REVERT: A 413 MET cc_start: 0.7971 (tpp) cc_final: 0.7510 (mmm) REVERT: A 420 GLU cc_start: 0.8188 (tt0) cc_final: 0.7934 (tp30) REVERT: K 54 SER cc_start: 0.7550 (p) cc_final: 0.7026 (t) REVERT: K 149 PHE cc_start: 0.8348 (t80) cc_final: 0.8016 (t80) REVERT: K 203 MET cc_start: 0.8786 (mmp) cc_final: 0.8230 (ttm) REVERT: K 205 ASP cc_start: 0.7097 (t0) cc_final: 0.6099 (m-30) REVERT: K 218 ASP cc_start: 0.8408 (m-30) cc_final: 0.7861 (t0) REVERT: K 267 PHE cc_start: 0.8972 (m-80) cc_final: 0.8577 (m-80) REVERT: K 315 CYS cc_start: 0.9187 (t) cc_final: 0.8485 (t) REVERT: K 377 MET cc_start: 0.7916 (ttt) cc_final: 0.7621 (tmm) REVERT: K 390 ARG cc_start: 0.8621 (pmt-80) cc_final: 0.8397 (pmt-80) REVERT: K 420 GLU cc_start: 0.7942 (tt0) cc_final: 0.7671 (tp30) REVERT: B 21 TRP cc_start: 0.9063 (m100) cc_final: 0.8223 (m100) REVERT: B 181 GLU cc_start: 0.8861 (pt0) cc_final: 0.8328 (pp20) REVERT: B 291 GLN cc_start: 0.8465 (mt0) cc_final: 0.8215 (mt0) REVERT: B 293 MET cc_start: 0.7300 (pmm) cc_final: 0.6739 (pmm) REVERT: B 297 LYS cc_start: 0.8758 (ptpt) cc_final: 0.8436 (mmtm) REVERT: B 323 MET cc_start: 0.7225 (mpp) cc_final: 0.6858 (mpp) REVERT: B 406 MET cc_start: 0.8410 (mmm) cc_final: 0.8141 (mmm) REVERT: B 415 MET cc_start: 0.8793 (tpt) cc_final: 0.8505 (mmm) REVERT: F 85 PHE cc_start: 0.8406 (m-80) cc_final: 0.7978 (m-80) REVERT: F 90 PHE cc_start: 0.8254 (m-80) cc_final: 0.8027 (m-80) REVERT: F 164 MET cc_start: 0.8103 (mpp) cc_final: 0.7569 (mpp) REVERT: F 216 LYS cc_start: 0.8458 (mmtp) cc_final: 0.7999 (mmtm) REVERT: F 233 MET cc_start: 0.9208 (mtp) cc_final: 0.8956 (mtm) REVERT: F 403 MET cc_start: 0.5948 (mmt) cc_final: 0.5619 (mmt) REVERT: G 6 HIS cc_start: 0.8954 (t70) cc_final: 0.8625 (t70) REVERT: G 83 GLN cc_start: 0.8465 (mp10) cc_final: 0.7681 (tm-30) REVERT: G 164 MET cc_start: 0.8370 (mpp) cc_final: 0.7855 (mpp) REVERT: G 180 VAL cc_start: 0.8778 (m) cc_final: 0.8480 (p) REVERT: G 216 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8181 (mmtm) REVERT: G 228 LEU cc_start: 0.9151 (mm) cc_final: 0.8821 (tp) REVERT: G 233 MET cc_start: 0.9057 (mtp) cc_final: 0.8632 (mtm) REVERT: G 321 MET cc_start: 0.8281 (ptp) cc_final: 0.7697 (ptp) REVERT: G 332 ASN cc_start: 0.7582 (m-40) cc_final: 0.7152 (p0) REVERT: G 406 MET cc_start: 0.8640 (mmm) cc_final: 0.8293 (tpt) REVERT: D 58 LYS cc_start: 0.7824 (ttmm) cc_final: 0.7481 (mtpp) REVERT: D 163 ILE cc_start: 0.8973 (pt) cc_final: 0.8596 (mp) REVERT: D 181 GLU cc_start: 0.8675 (pt0) cc_final: 0.8397 (pp20) REVERT: D 245 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7750 (mm-40) REVERT: D 299 MET cc_start: 0.9297 (mmp) cc_final: 0.8972 (mmm) REVERT: D 328 GLU cc_start: 0.8525 (tp30) cc_final: 0.8310 (tp30) REVERT: D 362 LYS cc_start: 0.9104 (tptt) cc_final: 0.8818 (tptp) REVERT: D 363 MET cc_start: 0.7842 (ptp) cc_final: 0.7603 (ptt) REVERT: I 118 ASP cc_start: 0.8614 (m-30) cc_final: 0.8161 (t70) REVERT: I 164 MET cc_start: 0.8010 (mpp) cc_final: 0.7700 (mpp) REVERT: I 242 PHE cc_start: 0.7652 (m-80) cc_final: 0.7286 (m-10) REVERT: I 293 MET cc_start: 0.7607 (pmm) cc_final: 0.7400 (pmm) REVERT: I 297 LYS cc_start: 0.8397 (ptpt) cc_final: 0.8029 (mptt) REVERT: I 299 MET cc_start: 0.9239 (mmm) cc_final: 0.8689 (mmm) REVERT: I 362 LYS cc_start: 0.9093 (tptt) cc_final: 0.8809 (tptp) REVERT: I 363 MET cc_start: 0.7990 (ptp) cc_final: 0.7677 (ptt) REVERT: H 180 VAL cc_start: 0.8953 (m) cc_final: 0.8721 (p) REVERT: H 233 MET cc_start: 0.9040 (mtm) cc_final: 0.8838 (mtm) REVERT: H 293 MET cc_start: 0.7915 (mtp) cc_final: 0.7389 (ptp) REVERT: H 323 MET cc_start: 0.7226 (mpp) cc_final: 0.7019 (mpp) REVERT: H 353 VAL cc_start: 0.8700 (t) cc_final: 0.8443 (t) outliers start: 0 outliers final: 0 residues processed: 820 average time/residue: 0.2297 time to fit residues: 319.8736 Evaluate side-chains 595 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 89 optimal weight: 20.0000 chunk 401 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 289 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 444 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 319 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 461 optimal weight: 7.9990 chunk 459 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 ASN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 ASN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 298 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN I 291 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.091919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.081407 restraints weight = 130994.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.083937 restraints weight = 75514.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.085731 restraints weight = 48544.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.087008 restraints weight = 33409.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.087937 restraints weight = 24272.665| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 41454 Z= 0.160 Angle : 0.595 8.533 56328 Z= 0.307 Chirality : 0.045 0.229 6162 Planarity : 0.004 0.054 7326 Dihedral : 11.547 178.352 5658 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.02 % Allowed : 0.60 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.12), residues: 5064 helix: -0.14 (0.11), residues: 2202 sheet: -0.35 (0.19), residues: 678 loop : -1.50 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 422 TYR 0.019 0.002 TYR A 24 PHE 0.022 0.002 PHE B 242 TRP 0.039 0.002 TRP B 101 HIS 0.008 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (41454) covalent geometry : angle 0.59473 / 0.31 (56328) hydrogen bonds : bond 0.03554 / 2.36 ( 1411) hydrogen bonds : angle 4.90432 / 3.45 ( 4107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 809 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7277 (ptm) cc_final: 0.6207 (tmm) REVERT: E 54 SER cc_start: 0.7305 (p) cc_final: 0.6824 (t) REVERT: E 149 PHE cc_start: 0.8135 (t80) cc_final: 0.7916 (t80) REVERT: E 205 ASP cc_start: 0.7397 (t0) cc_final: 0.6585 (m-30) REVERT: E 250 VAL cc_start: 0.8252 (t) cc_final: 0.7780 (t) REVERT: E 267 PHE cc_start: 0.9064 (m-80) cc_final: 0.8700 (m-80) REVERT: E 293 ASN cc_start: 0.8881 (m110) cc_final: 0.8354 (m110) REVERT: E 313 MET cc_start: 0.8065 (mtm) cc_final: 0.7010 (mtp) REVERT: E 326 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8134 (pttm) REVERT: E 351 PHE cc_start: 0.7832 (m-80) cc_final: 0.7350 (m-80) REVERT: J 205 ASP cc_start: 0.7655 (t0) cc_final: 0.6930 (m-30) REVERT: J 260 VAL cc_start: 0.8856 (t) cc_final: 0.8427 (p) REVERT: J 267 PHE cc_start: 0.9084 (m-80) cc_final: 0.8816 (m-80) REVERT: J 313 MET cc_start: 0.7741 (mtm) cc_final: 0.6573 (mtp) REVERT: J 352 LYS cc_start: 0.7868 (tptp) cc_final: 0.7474 (mmtt) REVERT: J 377 MET cc_start: 0.7922 (ttt) cc_final: 0.7369 (tmm) REVERT: C 36 MET cc_start: 0.7642 (ptm) cc_final: 0.6054 (tmm) REVERT: C 109 THR cc_start: 0.8963 (m) cc_final: 0.8272 (p) REVERT: C 203 MET cc_start: 0.8377 (mmp) cc_final: 0.8106 (mmm) REVERT: C 205 ASP cc_start: 0.7604 (t0) cc_final: 0.6857 (m-30) REVERT: C 301 GLN cc_start: 0.8890 (mt0) cc_final: 0.8309 (pt0) REVERT: C 313 MET cc_start: 0.7752 (mtm) cc_final: 0.6596 (mtp) REVERT: C 413 MET cc_start: 0.7904 (tpt) cc_final: 0.7632 (mmm) REVERT: L 36 MET cc_start: 0.7625 (ptm) cc_final: 0.6390 (tmm) REVERT: L 169 PHE cc_start: 0.8506 (m-80) cc_final: 0.8301 (m-80) REVERT: L 205 ASP cc_start: 0.7589 (t0) cc_final: 0.6803 (m-30) REVERT: L 260 VAL cc_start: 0.8868 (t) cc_final: 0.8389 (p) REVERT: L 301 GLN cc_start: 0.8662 (mt0) cc_final: 0.8358 (pt0) REVERT: A 36 MET cc_start: 0.6683 (ptm) cc_final: 0.5866 (tmm) REVERT: A 55 GLU cc_start: 0.8304 (tt0) cc_final: 0.7865 (pm20) REVERT: A 205 ASP cc_start: 0.7335 (t0) cc_final: 0.6534 (m-30) REVERT: A 255 PHE cc_start: 0.6883 (m-80) cc_final: 0.6627 (m-80) REVERT: A 260 VAL cc_start: 0.8963 (t) cc_final: 0.8486 (p) REVERT: A 316 CYS cc_start: 0.8304 (t) cc_final: 0.7758 (t) REVERT: A 351 PHE cc_start: 0.8106 (m-80) cc_final: 0.7601 (m-80) REVERT: A 377 MET cc_start: 0.8053 (ttp) cc_final: 0.7775 (ttp) REVERT: A 413 MET cc_start: 0.8007 (tpp) cc_final: 0.7570 (mmm) REVERT: A 420 GLU cc_start: 0.8222 (tt0) cc_final: 0.7934 (tp30) REVERT: K 54 SER cc_start: 0.7424 (p) cc_final: 0.6945 (t) REVERT: K 149 PHE cc_start: 0.8318 (t80) cc_final: 0.7972 (t80) REVERT: K 203 MET cc_start: 0.8708 (mmp) cc_final: 0.8249 (ttm) REVERT: K 205 ASP cc_start: 0.6998 (t0) cc_final: 0.6225 (m-30) REVERT: K 218 ASP cc_start: 0.8283 (m-30) cc_final: 0.7701 (t0) REVERT: K 267 PHE cc_start: 0.8897 (m-80) cc_final: 0.8582 (m-80) REVERT: K 315 CYS cc_start: 0.9131 (t) cc_final: 0.8430 (t) REVERT: K 377 MET cc_start: 0.7856 (ttt) cc_final: 0.7574 (tmm) REVERT: K 420 GLU cc_start: 0.7901 (tt0) cc_final: 0.7695 (tp30) REVERT: B 21 TRP cc_start: 0.8991 (m100) cc_final: 0.8327 (m100) REVERT: B 181 GLU cc_start: 0.8765 (pt0) cc_final: 0.8291 (pp20) REVERT: B 291 GLN cc_start: 0.8369 (mt0) cc_final: 0.8164 (mt0) REVERT: B 293 MET cc_start: 0.7165 (pmm) cc_final: 0.6838 (pmm) REVERT: B 297 LYS cc_start: 0.8749 (ptpt) cc_final: 0.8460 (mmtm) REVERT: B 299 MET cc_start: 0.9165 (mmm) cc_final: 0.8854 (mmm) REVERT: B 323 MET cc_start: 0.7109 (mpp) cc_final: 0.6843 (mpp) REVERT: B 363 MET cc_start: 0.8377 (mtm) cc_final: 0.8031 (mtm) REVERT: B 406 MET cc_start: 0.8416 (mmm) cc_final: 0.8174 (mmm) REVERT: F 111 GLU cc_start: 0.8509 (pp20) cc_final: 0.8223 (pp20) REVERT: F 216 LYS cc_start: 0.8362 (mmtp) cc_final: 0.7959 (mmtm) REVERT: F 233 MET cc_start: 0.9153 (mtp) cc_final: 0.8901 (mtm) REVERT: F 323 MET cc_start: 0.7567 (mpp) cc_final: 0.7348 (mpp) REVERT: F 379 LYS cc_start: 0.8370 (mtmm) cc_final: 0.7895 (pttp) REVERT: G 6 HIS cc_start: 0.8952 (t70) cc_final: 0.8720 (t70) REVERT: G 83 GLN cc_start: 0.8468 (mp10) cc_final: 0.7688 (tm-30) REVERT: G 164 MET cc_start: 0.8381 (mpp) cc_final: 0.7903 (mpp) REVERT: G 216 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8124 (mmtm) REVERT: G 228 LEU cc_start: 0.9109 (mm) cc_final: 0.8812 (tp) REVERT: G 321 MET cc_start: 0.8272 (ptp) cc_final: 0.7791 (ptp) REVERT: G 406 MET cc_start: 0.8556 (mmm) cc_final: 0.8278 (tpt) REVERT: D 58 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7434 (mtpp) REVERT: D 163 ILE cc_start: 0.8974 (pt) cc_final: 0.8632 (mp) REVERT: D 245 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7752 (mm-40) REVERT: D 257 MET cc_start: 0.8920 (mtm) cc_final: 0.8480 (mtp) REVERT: D 299 MET cc_start: 0.9198 (mmp) cc_final: 0.8903 (mmm) REVERT: D 328 GLU cc_start: 0.8455 (tp30) cc_final: 0.8248 (tp30) REVERT: I 118 ASP cc_start: 0.8524 (m-30) cc_final: 0.8071 (t70) REVERT: I 164 MET cc_start: 0.8018 (mpp) cc_final: 0.7778 (mpp) REVERT: I 242 PHE cc_start: 0.7668 (m-80) cc_final: 0.7289 (m-10) REVERT: I 293 MET cc_start: 0.7685 (pmm) cc_final: 0.7480 (pmm) REVERT: I 297 LYS cc_start: 0.8396 (ptpt) cc_final: 0.8062 (mptt) REVERT: I 299 MET cc_start: 0.9207 (mmm) cc_final: 0.8709 (mmm) REVERT: I 362 LYS cc_start: 0.9072 (tptt) cc_final: 0.8776 (tptp) REVERT: I 363 MET cc_start: 0.7972 (ptp) cc_final: 0.7709 (ptt) REVERT: H 180 VAL cc_start: 0.8906 (m) cc_final: 0.8684 (p) REVERT: H 233 MET cc_start: 0.8988 (mtm) cc_final: 0.8732 (mtm) REVERT: H 293 MET cc_start: 0.7920 (mtp) cc_final: 0.7352 (ptp) REVERT: H 353 VAL cc_start: 0.8759 (t) cc_final: 0.8508 (t) outliers start: 1 outliers final: 0 residues processed: 810 average time/residue: 0.2372 time to fit residues: 325.9935 Evaluate side-chains 586 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 193 optimal weight: 9.9990 chunk 490 optimal weight: 7.9990 chunk 356 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 283 optimal weight: 20.0000 chunk 433 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 chunk 363 optimal weight: 20.0000 chunk 365 optimal weight: 8.9990 chunk 467 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 298 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 ASN I 291 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN H 298 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.091383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080967 restraints weight = 130299.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.083502 restraints weight = 75318.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.085251 restraints weight = 48312.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.086514 restraints weight = 33421.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.087393 restraints weight = 24328.552| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 41454 Z= 0.162 Angle : 0.603 9.053 56328 Z= 0.310 Chirality : 0.046 0.211 6162 Planarity : 0.004 0.060 7326 Dihedral : 11.526 178.770 5658 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 5064 helix: -0.14 (0.11), residues: 2196 sheet: -0.23 (0.19), residues: 708 loop : -1.43 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 422 TYR 0.017 0.002 TYR D 340 PHE 0.028 0.002 PHE H 266 TRP 0.028 0.002 TRP D 101 HIS 0.007 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (41454) covalent geometry : angle 0.60259 / 0.31 (56328) hydrogen bonds : bond 0.03538 / 2.35 ( 1411) hydrogen bonds : angle 4.91106 / 3.45 ( 4107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 790 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7558 (ptm) cc_final: 0.6265 (tmm) REVERT: E 54 SER cc_start: 0.7444 (p) cc_final: 0.6929 (t) REVERT: E 149 PHE cc_start: 0.8172 (t80) cc_final: 0.7915 (t80) REVERT: E 205 ASP cc_start: 0.7483 (t0) cc_final: 0.6529 (m-30) REVERT: E 267 PHE cc_start: 0.9150 (m-80) cc_final: 0.8749 (m-80) REVERT: E 293 ASN cc_start: 0.8837 (m110) cc_final: 0.8456 (m110) REVERT: E 313 MET cc_start: 0.8170 (mtm) cc_final: 0.7095 (mtp) REVERT: E 326 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8156 (pttm) REVERT: E 351 PHE cc_start: 0.7842 (m-80) cc_final: 0.7319 (m-80) REVERT: J 203 MET cc_start: 0.8624 (mmp) cc_final: 0.8105 (ttp) REVERT: J 205 ASP cc_start: 0.7827 (t0) cc_final: 0.7011 (m-30) REVERT: J 260 VAL cc_start: 0.8874 (t) cc_final: 0.8455 (p) REVERT: J 267 PHE cc_start: 0.9096 (m-80) cc_final: 0.8818 (m-80) REVERT: J 313 MET cc_start: 0.7813 (mtm) cc_final: 0.6651 (mtp) REVERT: J 352 LYS cc_start: 0.7722 (tptp) cc_final: 0.7496 (mmtt) REVERT: J 377 MET cc_start: 0.7941 (ttt) cc_final: 0.7367 (tmm) REVERT: C 36 MET cc_start: 0.7765 (ptm) cc_final: 0.6130 (tmm) REVERT: C 203 MET cc_start: 0.8417 (mmp) cc_final: 0.8156 (mmm) REVERT: C 205 ASP cc_start: 0.7778 (t0) cc_final: 0.6789 (m-30) REVERT: C 313 MET cc_start: 0.7866 (mtm) cc_final: 0.6665 (mtp) REVERT: C 413 MET cc_start: 0.7877 (tpt) cc_final: 0.7574 (mmm) REVERT: L 36 MET cc_start: 0.7887 (ptm) cc_final: 0.6423 (tmm) REVERT: L 52 PHE cc_start: 0.8604 (m-10) cc_final: 0.8366 (m-10) REVERT: L 169 PHE cc_start: 0.8530 (m-80) cc_final: 0.8322 (m-80) REVERT: L 205 ASP cc_start: 0.7613 (t0) cc_final: 0.6735 (m-30) REVERT: L 260 VAL cc_start: 0.8903 (t) cc_final: 0.8453 (p) REVERT: L 301 GLN cc_start: 0.8853 (mt0) cc_final: 0.8325 (pm20) REVERT: L 313 MET cc_start: 0.7710 (mtm) cc_final: 0.7450 (mtm) REVERT: A 36 MET cc_start: 0.6844 (ptm) cc_final: 0.5972 (tmm) REVERT: A 55 GLU cc_start: 0.8415 (tt0) cc_final: 0.7920 (pm20) REVERT: A 205 ASP cc_start: 0.7392 (t0) cc_final: 0.6503 (m-30) REVERT: A 316 CYS cc_start: 0.8354 (t) cc_final: 0.7672 (t) REVERT: A 351 PHE cc_start: 0.8101 (m-80) cc_final: 0.7527 (m-80) REVERT: A 377 MET cc_start: 0.8172 (ttp) cc_final: 0.7795 (ttp) REVERT: A 413 MET cc_start: 0.8018 (tpp) cc_final: 0.7580 (mmm) REVERT: A 420 GLU cc_start: 0.8287 (tt0) cc_final: 0.7976 (tp30) REVERT: K 54 SER cc_start: 0.7646 (p) cc_final: 0.7043 (t) REVERT: K 149 PHE cc_start: 0.8378 (t80) cc_final: 0.8111 (t80) REVERT: K 203 MET cc_start: 0.8769 (mmp) cc_final: 0.8220 (ttm) REVERT: K 205 ASP cc_start: 0.7179 (t0) cc_final: 0.6213 (m-30) REVERT: K 218 ASP cc_start: 0.8250 (m-30) cc_final: 0.7816 (t0) REVERT: K 267 PHE cc_start: 0.8939 (m-80) cc_final: 0.8586 (m-80) REVERT: K 315 CYS cc_start: 0.9146 (t) cc_final: 0.8381 (t) REVERT: K 377 MET cc_start: 0.7938 (ttt) cc_final: 0.7585 (tmm) REVERT: K 420 GLU cc_start: 0.8003 (tt0) cc_final: 0.7733 (tp30) REVERT: B 293 MET cc_start: 0.7296 (pmm) cc_final: 0.6866 (pmm) REVERT: B 297 LYS cc_start: 0.8718 (ptpt) cc_final: 0.8448 (mmtm) REVERT: B 299 MET cc_start: 0.9194 (mmm) cc_final: 0.8831 (mmm) REVERT: B 323 MET cc_start: 0.7313 (mpp) cc_final: 0.6923 (mpp) REVERT: B 363 MET cc_start: 0.8369 (mtm) cc_final: 0.8065 (mtm) REVERT: B 406 MET cc_start: 0.8550 (mmm) cc_final: 0.8223 (mmm) REVERT: F 216 LYS cc_start: 0.8442 (mmtp) cc_final: 0.8022 (mmtm) REVERT: F 233 MET cc_start: 0.9184 (mtp) cc_final: 0.8934 (mtm) REVERT: F 379 LYS cc_start: 0.8388 (mtmm) cc_final: 0.7951 (pttp) REVERT: G 6 HIS cc_start: 0.8946 (t70) cc_final: 0.8707 (t70) REVERT: G 83 GLN cc_start: 0.8426 (mp10) cc_final: 0.7691 (tm-30) REVERT: G 101 TRP cc_start: 0.7392 (t60) cc_final: 0.7050 (t60) REVERT: G 164 MET cc_start: 0.8336 (mpp) cc_final: 0.7872 (mpp) REVERT: G 216 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8207 (mmtm) REVERT: G 228 LEU cc_start: 0.9123 (mm) cc_final: 0.8798 (tp) REVERT: G 321 MET cc_start: 0.8318 (ptp) cc_final: 0.7821 (ptp) REVERT: G 406 MET cc_start: 0.8668 (mmm) cc_final: 0.8365 (tpt) REVERT: G 414 ASN cc_start: 0.8732 (m110) cc_final: 0.8529 (m-40) REVERT: D 58 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7450 (mtpp) REVERT: D 163 ILE cc_start: 0.8999 (pt) cc_final: 0.8622 (mp) REVERT: D 245 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7775 (mm-40) REVERT: D 293 MET cc_start: 0.7768 (pmm) cc_final: 0.7528 (pmm) REVERT: D 299 MET cc_start: 0.9199 (mmp) cc_final: 0.8911 (mmm) REVERT: D 328 GLU cc_start: 0.8526 (tp30) cc_final: 0.8277 (tp30) REVERT: I 118 ASP cc_start: 0.8568 (m-30) cc_final: 0.8097 (t70) REVERT: I 149 THR cc_start: 0.9211 (p) cc_final: 0.8933 (p) REVERT: I 164 MET cc_start: 0.8210 (mpp) cc_final: 0.8008 (mpp) REVERT: I 198 GLU cc_start: 0.8466 (pt0) cc_final: 0.8241 (pt0) REVERT: I 242 PHE cc_start: 0.7705 (m-80) cc_final: 0.7348 (m-10) REVERT: I 293 MET cc_start: 0.7733 (pmm) cc_final: 0.7469 (pmm) REVERT: I 297 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8059 (mptt) REVERT: I 299 MET cc_start: 0.9276 (mmm) cc_final: 0.8723 (mmm) REVERT: I 362 LYS cc_start: 0.9085 (tptt) cc_final: 0.8764 (tptp) REVERT: I 363 MET cc_start: 0.7937 (ptp) cc_final: 0.7671 (ptt) REVERT: H 180 VAL cc_start: 0.8952 (m) cc_final: 0.8710 (p) REVERT: H 233 MET cc_start: 0.9021 (mtm) cc_final: 0.8769 (mtm) REVERT: H 253 LEU cc_start: 0.9414 (pp) cc_final: 0.9049 (pp) REVERT: H 257 MET cc_start: 0.8589 (ptp) cc_final: 0.8090 (ptp) REVERT: H 293 MET cc_start: 0.7970 (mtp) cc_final: 0.7371 (ptp) REVERT: H 353 VAL cc_start: 0.8772 (t) cc_final: 0.8513 (t) outliers start: 0 outliers final: 0 residues processed: 790 average time/residue: 0.2308 time to fit residues: 309.4852 Evaluate side-chains 590 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 251 optimal weight: 8.9990 chunk 364 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 113 optimal weight: 0.0570 chunk 366 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 459 optimal weight: 0.7980 chunk 396 optimal weight: 2.9990 chunk 379 optimal weight: 9.9990 overall best weight: 3.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** L 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 298 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN I 291 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.092835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.082277 restraints weight = 129707.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.084834 restraints weight = 74933.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.086644 restraints weight = 48166.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.087918 restraints weight = 33158.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.088848 restraints weight = 24152.760| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41454 Z= 0.123 Angle : 0.580 12.152 56328 Z= 0.296 Chirality : 0.045 0.237 6162 Planarity : 0.004 0.057 7326 Dihedral : 11.409 179.217 5658 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.02 % Allowed : 0.18 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.12), residues: 5064 helix: -0.08 (0.11), residues: 2226 sheet: -0.06 (0.19), residues: 696 loop : -1.46 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 2 TYR 0.034 0.001 TYR L 24 PHE 0.022 0.001 PHE C 149 TRP 0.028 0.002 TRP D 101 HIS 0.007 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (41454) covalent geometry : angle 0.58023 / 0.30 (56328) hydrogen bonds : bond 0.03339 / 2.22 ( 1411) hydrogen bonds : angle 4.74387 / 3.33 ( 4107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7455.55 seconds wall clock time: 130 minutes 1.34 seconds (7801.34 seconds total)