Starting phenix.real_space_refine on Sat Mar 7 04:09:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f67_31475/03_2026/7f67_31475.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f67_31475/03_2026/7f67_31475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f67_31475/03_2026/7f67_31475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f67_31475/03_2026/7f67_31475.map" model { file = "/net/cci-nas-00/data/ceres_data/7f67_31475/03_2026/7f67_31475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f67_31475/03_2026/7f67_31475.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 23787 2.51 5 N 6732 2.21 5 O 7038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37725 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2268 Classifications: {'peptide': 292} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2268 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2555 Classifications: {'peptide': 327} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 2 Chain: "D" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2536 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 310} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1793 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 93 Chain: "F" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1806 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 228} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "G" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2763 Classifications: {'peptide': 356} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 337} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2765 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 336} Chain: "I" Number of atoms: 4152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4152 Classifications: {'peptide': 591} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 736 Unresolved non-hydrogen dihedrals: 477 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 8, 'GLU:plan': 18, 'ASP:plan': 9, 'PHE:plan': 9, 'GLN:plan1': 13, 'TYR:plan': 5, 'HIS:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 336 Chain: "J" Number of atoms: 4139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4139 Classifications: {'peptide': 591} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 155} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 588 Unresolved non-hydrogen angles: 751 Unresolved non-hydrogen dihedrals: 484 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 9, 'ASP:plan': 10, 'GLU:plan': 20, 'PHE:plan': 9, 'GLN:plan1': 13, 'TYR:plan': 5, 'HIS:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 348 Chain: "K" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1528 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 2 Chain: "L" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ARG:plan': 18, 'GLU:plan': 25, 'ASP:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 296 Chain: "O" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2096 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1075 Unresolved non-hydrogen angles: 1375 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'ASP:plan': 15, 'HIS:plan': 9, 'GLU:plan': 26, 'ARG:plan': 19, 'GLN:plan1': 13, 'ASN:plan1': 14, 'PHE:plan': 6, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 443 Chain: "Q" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ARG:plan': 18, 'GLU:plan': 25, 'ASP:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 296 Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2096 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1075 Unresolved non-hydrogen angles: 1375 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'ASP:plan': 15, 'HIS:plan': 9, 'GLU:plan': 26, 'ARG:plan': 19, 'GLN:plan1': 13, 'ASN:plan1': 14, 'PHE:plan': 6, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 443 Time building chain proxies: 8.76, per 1000 atoms: 0.23 Number of scatterers: 37725 At special positions: 0 Unit cell: (164.971, 249.529, 191.499, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 7038 8.00 N 6732 7.00 C 23787 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 seconds 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10184 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 46 sheets defined 46.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.766A pdb=" N ASP A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'A' and resid 62 through 82 removed outlier: 3.734A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 116 removed outlier: 3.754A pdb=" N CYS A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.752A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 188 removed outlier: 3.869A pdb=" N GLU A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 3.670A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.565A pdb=" N LYS A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.978A pdb=" N VAL A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.716A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 41 through 58 removed outlier: 3.665A pdb=" N GLU B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 83 removed outlier: 3.965A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 105 removed outlier: 4.416A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.948A pdb=" N LYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.653A pdb=" N LYS B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 294 through 303 removed outlier: 4.042A pdb=" N ASP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.581A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.701A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.606A pdb=" N GLU C 157 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 210 removed outlier: 4.035A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 4.007A pdb=" N SER C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.766A pdb=" N LEU C 274 " --> pdb=" O MET C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.564A pdb=" N GLU C 281 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU C 282 " --> pdb=" O PRO C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.504A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.629A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 30 through 49 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.823A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 129 through 146 removed outlier: 3.853A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.226A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.531A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 227 removed outlier: 4.219A pdb=" N SER D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.663A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.567A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 342 removed outlier: 3.719A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'E' and resid 36 through 46 removed outlier: 3.564A pdb=" N LEU E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.508A pdb=" N GLU E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 94 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 114 through 124 removed outlier: 3.604A pdb=" N TYR E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.643A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 236 removed outlier: 4.890A pdb=" N ILE E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 277 through 295 removed outlier: 4.244A pdb=" N ARG E 289 " --> pdb=" O CYS E 285 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER E 294 " --> pdb=" O TRP E 290 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 46 Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.972A pdb=" N GLU F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'F' and resid 114 through 124 removed outlier: 4.793A pdb=" N LEU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.523A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 278 through 292 removed outlier: 4.244A pdb=" N TRP F 282 " --> pdb=" O TYR F 278 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 Processing helix chain 'G' and resid 191 through 196 Processing helix chain 'G' and resid 205 through 216 removed outlier: 3.821A pdb=" N LEU G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 240 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.703A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 287 Processing helix chain 'G' and resid 292 through 327 removed outlier: 4.600A pdb=" N LEU G 314 " --> pdb=" O GLU G 310 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ALA G 315 " --> pdb=" O LYS G 311 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS G 326 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 352 Processing helix chain 'G' and resid 368 through 379 removed outlier: 4.139A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 396 through 398 No H-bonds generated for 'chain 'G' and resid 396 through 398' Processing helix chain 'G' and resid 419 through 430 Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 459 through 464 Processing helix chain 'G' and resid 475 through 479 Processing helix chain 'G' and resid 493 through 497 Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 511 through 520 removed outlier: 3.507A pdb=" N SER G 520 " --> pdb=" O LEU G 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.622A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 240 Processing helix chain 'H' and resid 247 through 267 removed outlier: 3.605A pdb=" N ASP H 251 " --> pdb=" O GLU H 247 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 286 Processing helix chain 'H' and resid 292 through 312 Processing helix chain 'H' and resid 312 through 327 removed outlier: 4.063A pdb=" N GLN H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS H 326 " --> pdb=" O PHE H 322 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 327 " --> pdb=" O ALA H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 353 removed outlier: 3.537A pdb=" N GLY H 353 " --> pdb=" O ALA H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 379 removed outlier: 3.991A pdb=" N THR H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 395 Processing helix chain 'H' and resid 396 through 398 No H-bonds generated for 'chain 'H' and resid 396 through 398' Processing helix chain 'H' and resid 418 through 430 removed outlier: 4.733A pdb=" N GLN H 422 " --> pdb=" O VAL H 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 459 through 464 Processing helix chain 'H' and resid 475 through 479 Processing helix chain 'H' and resid 493 through 497 Processing helix chain 'H' and resid 508 through 510 No H-bonds generated for 'chain 'H' and resid 508 through 510' Processing helix chain 'H' and resid 511 through 519 removed outlier: 3.507A pdb=" N VAL H 515 " --> pdb=" O SER H 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 74 through 87 Processing helix chain 'I' and resid 98 through 108 removed outlier: 3.578A pdb=" N ILE I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.544A pdb=" N CYS I 112 " --> pdb=" O SER I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 161 through 176 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.608A pdb=" N GLN I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER I 234 " --> pdb=" O LEU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 263 removed outlier: 3.806A pdb=" N ALA I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 279 Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 550 through 568 Processing helix chain 'I' and resid 570 through 586 Processing helix chain 'I' and resid 588 through 608 Proline residue: I 604 - end of helix removed outlier: 3.743A pdb=" N MET I 608 " --> pdb=" O PRO I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 613 through 636 removed outlier: 3.909A pdb=" N TYR I 617 " --> pdb=" O ASP I 613 " (cutoff:3.500A) Proline residue: I 623 - end of helix removed outlier: 3.580A pdb=" N ALA I 627 " --> pdb=" O PRO I 623 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER I 629 " --> pdb=" O LEU I 625 " (cutoff:3.500A) Proline residue: I 630 - end of helix Processing helix chain 'I' and resid 638 through 656 removed outlier: 3.509A pdb=" N GLU I 655 " --> pdb=" O ASP I 651 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 673 removed outlier: 3.633A pdb=" N ILE I 661 " --> pdb=" O GLU I 657 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER I 662 " --> pdb=" O ALA I 658 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS I 665 " --> pdb=" O ILE I 661 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE I 670 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR I 671 " --> pdb=" O LEU I 667 " (cutoff:3.500A) Processing helix chain 'I' and resid 677 through 687 Processing helix chain 'I' and resid 693 through 699 removed outlier: 3.852A pdb=" N LEU I 697 " --> pdb=" O LYS I 693 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS I 699 " --> pdb=" O GLN I 695 " (cutoff:3.500A) Processing helix chain 'I' and resid 700 through 715 Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.657A pdb=" N ILE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 161 through 176 Processing helix chain 'J' and resid 228 through 234 removed outlier: 3.896A pdb=" N SER J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 263 removed outlier: 3.784A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 322 through 326 removed outlier: 3.529A pdb=" N ASN J 326 " --> pdb=" O PRO J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 550 through 568 Processing helix chain 'J' and resid 570 through 586 Processing helix chain 'J' and resid 588 through 607 Proline residue: J 604 - end of helix Processing helix chain 'J' and resid 613 through 628 removed outlier: 3.538A pdb=" N TYR J 617 " --> pdb=" O ASP J 613 " (cutoff:3.500A) Proline residue: J 623 - end of helix removed outlier: 3.781A pdb=" N ALA J 627 " --> pdb=" O PRO J 623 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP J 628 " --> pdb=" O LEU J 624 " (cutoff:3.500A) Processing helix chain 'J' and resid 628 through 636 Processing helix chain 'J' and resid 638 through 656 Processing helix chain 'J' and resid 656 through 661 removed outlier: 4.252A pdb=" N ILE J 661 " --> pdb=" O GLU J 657 " (cutoff:3.500A) Processing helix chain 'J' and resid 662 through 673 removed outlier: 3.659A pdb=" N MET J 668 " --> pdb=" O ALA J 664 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE J 670 " --> pdb=" O VAL J 666 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR J 671 " --> pdb=" O LEU J 667 " (cutoff:3.500A) Processing helix chain 'J' and resid 677 through 687 Processing helix chain 'J' and resid 693 through 699 Processing helix chain 'J' and resid 700 through 715 Processing helix chain 'K' and resid 61 through 66 removed outlier: 3.793A pdb=" N TYR K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 removed outlier: 4.276A pdb=" N ALA K 94 " --> pdb=" O PHE K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 117 Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.588A pdb=" N SER K 130 " --> pdb=" O CYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 154 removed outlier: 4.033A pdb=" N LEU K 146 " --> pdb=" O THR K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 178 Processing helix chain 'K' and resid 180 through 184 Processing helix chain 'K' and resid 188 through 204 removed outlier: 3.594A pdb=" N ALA K 204 " --> pdb=" O ARG K 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 3 No H-bonds generated for 'chain 'L' and resid 1 through 3' Processing helix chain 'L' and resid 61 through 66 removed outlier: 3.975A pdb=" N TYR L 65 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 97 removed outlier: 3.690A pdb=" N ALA L 94 " --> pdb=" O PHE L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 119 removed outlier: 4.464A pdb=" N TRP L 119 " --> pdb=" O LYS L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.969A pdb=" N SER L 130 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 153 Processing helix chain 'L' and resid 158 through 177 Processing helix chain 'L' and resid 180 through 184 Processing helix chain 'L' and resid 188 through 204 Processing helix chain 'N' and resid 36 through 39 removed outlier: 3.763A pdb=" N ASN N 39 " --> pdb=" O LEU N 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 36 through 39' Processing helix chain 'N' and resid 48 through 50 No H-bonds generated for 'chain 'N' and resid 48 through 50' Processing helix chain 'N' and resid 57 through 61 Processing helix chain 'N' and resid 90 through 119 Processing helix chain 'N' and resid 122 through 133 Processing helix chain 'N' and resid 134 through 142 Processing helix chain 'N' and resid 145 through 158 removed outlier: 3.682A pdb=" N TYR N 149 " --> pdb=" O GLY N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 164 Processing helix chain 'N' and resid 169 through 183 Processing helix chain 'N' and resid 202 through 216 Processing helix chain 'N' and resid 242 through 264 removed outlier: 3.664A pdb=" N SER N 248 " --> pdb=" O THR N 244 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 13 Processing helix chain 'S' and resid 53 through 62 removed outlier: 4.205A pdb=" N VAL S 57 " --> pdb=" O GLY S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 146 removed outlier: 3.804A pdb=" N LEU S 141 " --> pdb=" O GLY S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 179 removed outlier: 3.821A pdb=" N GLN S 169 " --> pdb=" O CYS S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 195 through 214 Processing helix chain 'S' and resid 229 through 243 Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 48 through 50 No H-bonds generated for 'chain 'Q' and resid 48 through 50' Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 90 through 119 Processing helix chain 'Q' and resid 122 through 133 Processing helix chain 'Q' and resid 134 through 142 Processing helix chain 'Q' and resid 145 through 158 Processing helix chain 'Q' and resid 159 through 165 removed outlier: 3.680A pdb=" N LEU Q 165 " --> pdb=" O ILE Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 183 Processing helix chain 'Q' and resid 202 through 217 Processing helix chain 'Q' and resid 242 through 264 removed outlier: 3.822A pdb=" N LYS Q 264 " --> pdb=" O LYS Q 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 12 Processing helix chain 'T' and resid 53 through 62 Processing helix chain 'T' and resid 137 through 146 removed outlier: 3.648A pdb=" N LEU T 141 " --> pdb=" O GLY T 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 179 removed outlier: 3.657A pdb=" N GLN T 169 " --> pdb=" O CYS T 165 " (cutoff:3.500A) Processing helix chain 'T' and resid 195 through 214 Processing helix chain 'T' and resid 229 through 243 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 removed outlier: 3.524A pdb=" N LEU A 192 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 126 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA3, first strand: chain 'B' and resid 175 through 178 removed outlier: 6.222A pdb=" N ALA B 123 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N TYR B 151 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR B 153 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR B 124 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE B 194 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU B 126 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE B 226 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE B 285 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 228 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AA5, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.425A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLU C 163 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE C 190 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AA7, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.400A pdb=" N SER C 307 " --> pdb=" O TYR H 385 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LEU H 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE H 333 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL H 361 " --> pdb=" O ILE H 333 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL H 335 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL H 332 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU H 402 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU H 334 " --> pdb=" O LEU H 402 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLY H 404 " --> pdb=" O LEU H 334 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR H 336 " --> pdb=" O GLY H 404 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N CYS H 437 " --> pdb=" O VAL H 401 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU H 403 " --> pdb=" O CYS H 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.699A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.372A pdb=" N SER D 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU G 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE G 333 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL G 361 " --> pdb=" O ILE G 333 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL G 335 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL G 332 " --> pdb=" O LYS G 400 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU G 402 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU G 334 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLY G 404 " --> pdb=" O LEU G 334 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR G 336 " --> pdb=" O GLY G 404 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ILE G 501 " --> pdb=" O VAL G 434 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.564A pdb=" N GLN E 4 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 104 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 6 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER E 105 " --> pdb=" O HIS E 203 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N HIS E 203 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU E 131 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU E 204 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA E 129 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 167 through 172 removed outlier: 6.664A pdb=" N GLY E 159 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET E 170 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE E 157 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL I 238 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL I 202 " --> pdb=" O PHE I 215 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE I 215 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA I 204 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG I 211 " --> pdb=" O ASP I 206 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE I 287 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N MET I 181 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N HIS I 290 " --> pdb=" O MET I 181 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N MET I 183 " --> pdb=" O HIS I 290 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR I 292 " --> pdb=" O MET I 183 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE I 185 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE I 249 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS I 186 " --> pdb=" O CYS I 247 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS I 247 " --> pdb=" O LYS I 186 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N HIS I 248 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR I 152 " --> pdb=" O HIS I 248 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL I 151 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR I 91 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE I 123 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL I 93 " --> pdb=" O ILE I 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 179 through 183 Processing sheet with id=AB5, first strand: chain 'F' and resid 76 through 78 removed outlier: 8.164A pdb=" N ILE F 52 " --> pdb=" O PHE F 3 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA F 5 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL F 54 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL F 7 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU F 102 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER F 105 " --> pdb=" O HIS F 203 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N HIS F 203 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU F 131 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU F 204 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA F 129 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 167 through 172 removed outlier: 6.476A pdb=" N GLY F 159 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET F 170 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE F 157 " --> pdb=" O MET F 170 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP J 206 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL J 212 " --> pdb=" O ASP J 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 182 through 183 Processing sheet with id=AB8, first strand: chain 'G' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'H' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'H' and resid 466 through 467 Processing sheet with id=AC2, first strand: chain 'H' and resid 500 through 502 Processing sheet with id=AC3, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AC4, first strand: chain 'I' and resid 336 through 337 removed outlier: 6.327A pdb=" N LEU I 361 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL I 378 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR I 395 " --> pdb=" O LEU I 413 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU I 412 " --> pdb=" O LEU I 431 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL I 430 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.634A pdb=" N ILE I 355 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE I 373 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN I 407 " --> pdb=" O LEU I 425 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 384 through 385 removed outlier: 6.335A pdb=" N HIS I 384 " --> pdb=" O VAL I 402 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLU I 418 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'J' and resid 119 through 124 removed outlier: 3.611A pdb=" N VAL J 151 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR J 152 " --> pdb=" O HIS J 248 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N HIS J 248 " --> pdb=" O TYR J 152 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS J 247 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE J 184 " --> pdb=" O CYS J 247 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE J 249 " --> pdb=" O THR J 182 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR J 182 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU J 187 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AC9, first strand: chain 'J' and resid 336 through 338 removed outlier: 3.814A pdb=" N ILE J 342 " --> pdb=" O SER J 338 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL J 378 " --> pdb=" O LEU J 396 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR J 395 " --> pdb=" O LEU J 413 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU J 412 " --> pdb=" O LEU J 431 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL J 430 " --> pdb=" O ILE J 449 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 355 through 356 removed outlier: 6.690A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL J 390 " --> pdb=" O ILE J 408 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN J 407 " --> pdb=" O LEU J 425 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 384 through 385 removed outlier: 6.444A pdb=" N HIS J 384 " --> pdb=" O VAL J 402 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG J 401 " --> pdb=" O VAL J 419 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU J 418 " --> pdb=" O VAL J 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'K' and resid 5 through 13 removed outlier: 5.268A pdb=" N TYR K 5 " --> pdb=" O LYS K 32 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LYS K 32 " --> pdb=" O TYR K 5 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE K 7 " --> pdb=" O TYR K 30 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER K 24 " --> pdb=" O ASN K 13 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 44 through 47 removed outlier: 9.529A pdb=" N TRP K 74 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR K 40 " --> pdb=" O TRP K 74 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AD6, first strand: chain 'L' and resid 5 through 12 removed outlier: 5.443A pdb=" N TYR L 5 " --> pdb=" O LYS L 32 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS L 32 " --> pdb=" O TYR L 5 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 44 through 47 removed outlier: 9.870A pdb=" N TRP L 74 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR L 40 " --> pdb=" O TRP L 74 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.027A pdb=" N ARG L 52 " --> pdb=" O LEU L 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'N' and resid 19 through 26 removed outlier: 6.908A pdb=" N TYR N 32 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE N 26 " --> pdb=" O GLY N 30 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLU N 42 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N LEU N 84 " --> pdb=" O GLU N 42 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET N 44 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER N 85 " --> pdb=" O VAL N 72 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL N 72 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 225 through 227 removed outlier: 5.259A pdb=" N ASP N 193 " --> pdb=" O GLU N 273 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU N 273 " --> pdb=" O ASP N 193 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLU N 195 " --> pdb=" O GLN N 271 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN N 271 " --> pdb=" O GLU N 195 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA N 197 " --> pdb=" O ASN N 269 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN N 269 " --> pdb=" O ALA N 197 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 83 through 90 removed outlier: 6.582A pdb=" N LYS S 90 " --> pdb=" O LEU S 126 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU S 126 " --> pdb=" O LYS S 90 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LEU S 156 " --> pdb=" O ASN S 43 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY S 45 " --> pdb=" O LEU S 156 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 255 through 262 removed outlier: 6.653A pdb=" N ARG S 255 " --> pdb=" O LEU S 284 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY S 280 " --> pdb=" O ILE S 259 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER S 261 " --> pdb=" O VAL S 278 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL S 278 " --> pdb=" O SER S 261 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE S 314 " --> pdb=" O PRO S 298 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N SER S 316 " --> pdb=" O VAL S 296 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL S 296 " --> pdb=" O SER S 316 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE S 318 " --> pdb=" O ILE S 294 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE S 294 " --> pdb=" O ILE S 318 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL S 357 " --> pdb=" O ARG S 297 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN S 356 " --> pdb=" O VAL S 258 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 288 through 289 removed outlier: 3.529A pdb=" N LEU S 288 " --> pdb=" O ALA S 331 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 376 through 377 removed outlier: 6.770A pdb=" N LEU S 443 " --> pdb=" O ILE S 454 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TRP S 456 " --> pdb=" O ILE S 441 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE S 441 " --> pdb=" O TRP S 456 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA S 442 " --> pdb=" O ASN S 407 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN S 407 " --> pdb=" O ALA S 442 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET S 405 " --> pdb=" O SER S 444 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG S 446 " --> pdb=" O VAL S 403 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N VAL S 403 " --> pdb=" O ARG S 446 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N SER S 412 " --> pdb=" O PRO S 432 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLY S 414 " --> pdb=" O THR S 430 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG S 416 " --> pdb=" O VAL S 428 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL S 428 " --> pdb=" O ARG S 416 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS S 426 " --> pdb=" O SER S 418 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR S 369 " --> pdb=" O LEU S 429 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL S 463 " --> pdb=" O THR S 369 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU S 371 " --> pdb=" O ARG S 461 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG S 461 " --> pdb=" O LEU S 371 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE S 373 " --> pdb=" O ILE S 459 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE S 459 " --> pdb=" O ILE S 373 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 19 through 26 removed outlier: 6.986A pdb=" N TYR Q 32 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE Q 26 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY Q 30 " --> pdb=" O ILE Q 26 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU Q 42 " --> pdb=" O ILE Q 82 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N LEU Q 84 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET Q 44 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR Q 81 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL Q 75 " --> pdb=" O TYR Q 81 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP Q 83 " --> pdb=" O ILE Q 73 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 224 through 227 removed outlier: 5.043A pdb=" N ASP Q 193 " --> pdb=" O GLU Q 273 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU Q 273 " --> pdb=" O ASP Q 193 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU Q 195 " --> pdb=" O GLN Q 271 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN Q 271 " --> pdb=" O GLU Q 195 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA Q 197 " --> pdb=" O ASN Q 269 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN Q 269 " --> pdb=" O ALA Q 197 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 83 through 90 removed outlier: 6.514A pdb=" N LYS T 90 " --> pdb=" O LEU T 126 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU T 126 " --> pdb=" O LYS T 90 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE T 42 " --> pdb=" O HIS T 129 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN T 43 " --> pdb=" O ALA T 154 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU T 156 " --> pdb=" O ASN T 43 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY T 45 " --> pdb=" O LEU T 156 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 255 through 260 removed outlier: 5.481A pdb=" N VAL T 258 " --> pdb=" O SER T 282 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER T 282 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N MET T 310 " --> pdb=" O ILE T 300 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE T 300 " --> pdb=" O MET T 310 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS T 312 " --> pdb=" O PRO T 298 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE T 314 " --> pdb=" O VAL T 296 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL T 357 " --> pdb=" O ARG T 297 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN T 356 " --> pdb=" O VAL T 258 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 376 through 377 removed outlier: 6.825A pdb=" N LEU T 443 " --> pdb=" O ILE T 454 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TRP T 456 " --> pdb=" O ILE T 441 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE T 441 " --> pdb=" O TRP T 456 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA T 442 " --> pdb=" O ASN T 407 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN T 407 " --> pdb=" O ALA T 442 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG T 446 " --> pdb=" O VAL T 403 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N VAL T 403 " --> pdb=" O ARG T 446 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N SER T 412 " --> pdb=" O PRO T 432 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY T 414 " --> pdb=" O THR T 430 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N LEU T 429 " --> pdb=" O GLU T 372 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N GLU T 372 " --> pdb=" O LEU T 429 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N ASN T 431 " --> pdb=" O GLU T 370 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU T 370 " --> pdb=" O ASN T 431 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE T 368 " --> pdb=" O ILE T 465 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE T 465 " --> pdb=" O PHE T 368 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU T 370 " --> pdb=" O VAL T 463 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG T 461 " --> pdb=" O GLU T 372 " (cutoff:3.500A) 1903 hydrogen bonds defined for protein. 5352 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: 8.91 Time building geometry restraints manager: 4.20 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: 12848 1.34 - 1.46: 5290 1.46 - 1.58: 19897 1.58 - 1.70: 0 1.70 - 1.82: 259 Bond restraints: 38294 Sorted by residual: bond pdb=" CA TYR B 86 " pdb=" C TYR B 86 " ideal model delta sigma weight residual 1.523 1.488 0.036 1.30e-02 5.92e+03 7.54e+00 bond pdb=" CD2 TRP T 456 " pdb=" CE2 TRP T 456 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 5.01e+00 bond pdb=" CD2 TRP Q 135 " pdb=" CE2 TRP Q 135 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.87e+00 bond pdb=" CD2 TRP I 397 " pdb=" CE2 TRP I 397 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.86e+00 bond pdb=" CD2 TRP S 456 " pdb=" CE2 TRP S 456 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.80e+00 ... (remaining 38289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 51764 2.67 - 5.34: 297 5.34 - 8.01: 28 8.01 - 10.67: 1 10.67 - 13.34: 2 Bond angle restraints: 52092 Sorted by residual: angle pdb=" N SER B 84 " pdb=" CA SER B 84 " pdb=" C SER B 84 " ideal model delta sigma weight residual 114.62 119.51 -4.89 1.14e+00 7.69e-01 1.84e+01 angle pdb=" CD2 TRP T 451 " pdb=" CE3 TRP T 451 " pdb=" CZ3 TRP T 451 " ideal model delta sigma weight residual 118.60 124.04 -5.44 1.30e+00 5.92e-01 1.75e+01 angle pdb=" CD2 TRP T 456 " pdb=" CE3 TRP T 456 " pdb=" CZ3 TRP T 456 " ideal model delta sigma weight residual 118.60 124.04 -5.44 1.30e+00 5.92e-01 1.75e+01 angle pdb=" CD2 TRP J 628 " pdb=" CE3 TRP J 628 " pdb=" CZ3 TRP J 628 " ideal model delta sigma weight residual 118.60 124.01 -5.41 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CD2 TRP N 135 " pdb=" CE3 TRP N 135 " pdb=" CZ3 TRP N 135 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 ... (remaining 52087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 21217 17.46 - 34.93: 1509 34.93 - 52.39: 242 52.39 - 69.85: 41 69.85 - 87.32: 17 Dihedral angle restraints: 23026 sinusoidal: 7388 harmonic: 15638 Sorted by residual: dihedral pdb=" CA MET L 86 " pdb=" C MET L 86 " pdb=" N MET L 87 " pdb=" CA MET L 87 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA MET G 207 " pdb=" C MET G 207 " pdb=" N VAL G 208 " pdb=" CA VAL G 208 " ideal model delta harmonic sigma weight residual -180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU H 499 " pdb=" C LEU H 499 " pdb=" N VAL H 500 " pdb=" CA VAL H 500 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 23023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4821 0.049 - 0.098: 1097 0.098 - 0.147: 325 0.147 - 0.196: 9 0.196 - 0.244: 1 Chirality restraints: 6253 Sorted by residual: chirality pdb=" CA SER B 84 " pdb=" N SER B 84 " pdb=" C SER B 84 " pdb=" CB SER B 84 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CG LEU Q 126 " pdb=" CB LEU Q 126 " pdb=" CD1 LEU Q 126 " pdb=" CD2 LEU Q 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CA MET E 132 " pdb=" N MET E 132 " pdb=" C MET E 132 " pdb=" CB MET E 132 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.09e-01 ... (remaining 6250 not shown) Planarity restraints: 6802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE L 123 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO L 124 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO L 124 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 124 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO H 396 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 76 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ILE B 76 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE B 76 " 0.012 2.00e-02 2.50e+03 pdb=" N SER B 77 " 0.011 2.00e-02 2.50e+03 ... (remaining 6799 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1806 2.73 - 3.27: 39224 3.27 - 3.81: 61569 3.81 - 4.36: 68865 4.36 - 4.90: 120292 Nonbonded interactions: 291756 Sorted by model distance: nonbonded pdb=" OD2 ASP E 201 " pdb=" OH TYR E 205 " model vdw 2.187 3.040 nonbonded pdb=" OG SER A 61 " pdb=" O LYS A 249 " model vdw 2.199 3.040 nonbonded pdb=" OG SER F 105 " pdb=" OD1 ASP F 107 " model vdw 2.200 3.040 nonbonded pdb=" O THR J 332 " pdb=" OG SER J 364 " model vdw 2.223 3.040 nonbonded pdb=" NH2 ARG J 195 " pdb=" O TYR J 242 " model vdw 2.225 3.120 ... (remaining 291751 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 305)) selection = (chain 'B' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ )) or resid 45 through 305)) } ncs_group { reference = (chain 'C' and (resid 9 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ )) or resid 25 \ through 82 or (resid 83 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ )) or resid 84 through 98 or resid 10 \ 6 through 351)) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 9 or resid 28 through 55 or (resid 56 through 62 \ and (name N or name CA or name C or name O or name CB )) or resid 63 through 13 \ 4 or resid 136 through 268 or (resid 269 through 286 and (name N or name CA or n \ ame C or name O or name CB )) or resid 287 through 295)) selection = (chain 'F' and (resid 1 through 63 or (resid 64 through 74 and (name N or name C \ A or name C or name O or name CB )) or resid 75 through 79 or (resid 80 through \ 84 and (name N or name CA or name C or name O or name CB )) or resid 85 through \ 295)) } ncs_group { reference = (chain 'G' and resid 166 through 520) selection = (chain 'H' and (resid 166 through 169 or (resid 170 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ )) or resi \ d 171 through 187 or (resid 188 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name NE or name CZ )) or resid 189 through 291 or \ (resid 292 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ )) or resid 293 through 300 or (resid 301 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name CZ )) or resid 302 through 520)) } ncs_group { reference = (chain 'I' and (resid 40 through 228 or (resid 229 and (name N or name CA or nam \ e C or name O or name CB )) or resid 230 through 314 or (resid 315 through 316 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me NE or name CZ )) or resid 317 through 454 or (resid 455 through 458 and (name \ N or name CA or name C or name O or name CB )) or resid 459 through 715)) selection = (chain 'J' and (resid 40 through 396 or (resid 397 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or name \ CE2 or name CE3 or name CZ2 or name CZ3)) or resid 398 through 427 or (resid 428 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name NE or name CZ )) or resid 429 through 715)) } ncs_group { reference = (chain 'K' and (resid 1 through 117 or (resid 118 through 119 and (name N or nam \ e CA or name C or name O or name CB )) or resid 120 through 204)) selection = chain 'L' } ncs_group { reference = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' } 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: 6.030 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: 0.790 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 35.490 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.002 0.046 38294 Z= 0.120 Angle : 0.530 13.342 52092 Z= 0.290 Chirality : 0.043 0.244 6253 Planarity : 0.003 0.060 6802 Dihedral : 12.721 87.318 12842 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.09 % Allowed : 0.55 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.12), residues: 5274 helix: 2.01 (0.12), residues: 2074 sheet: -0.92 (0.18), residues: 824 loop : -0.93 (0.14), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 169 TYR 0.025 0.001 TYR G 259 PHE 0.029 0.001 PHE E 3 TRP 0.010 0.001 TRP H 476 HIS 0.003 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00227 (38294) covalent geometry : angle 0.52952 (52092) hydrogen bonds : bond 0.17196 ( 1903) hydrogen bonds : angle 5.71292 ( 5352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 266 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: C 81 MET cc_start: 0.9289 (mmp) cc_final: 0.8977 (mmp) REVERT: C 138 ASN cc_start: 0.8871 (m110) cc_final: 0.8582 (m110) REVERT: E 94 TYR cc_start: 0.9320 (t80) cc_final: 0.9053 (t80) REVERT: E 132 MET cc_start: 0.8739 (mmm) cc_final: 0.8441 (mmm) REVERT: F 71 MET cc_start: 0.8443 (ppp) cc_final: 0.7817 (ppp) REVERT: J 183 MET cc_start: 0.9482 (mmm) cc_final: 0.9211 (mtp) REVERT: K 69 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8726 (mt-10) REVERT: K 129 PHE cc_start: 0.8354 (m-80) cc_final: 0.7762 (m-80) REVERT: L 115 LYS cc_start: 0.7293 (pttm) cc_final: 0.7086 (tmtt) REVERT: N 7 PHE cc_start: 0.7784 (m-10) cc_final: 0.7424 (m-10) REVERT: N 44 MET cc_start: 0.8001 (mmm) cc_final: 0.7739 (mmm) REVERT: Q 22 ASN cc_start: 0.7805 (t0) cc_final: 0.7520 (t0) REVERT: Q 100 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8808 (tttt) outliers start: 3 outliers final: 3 residues processed: 269 average time/residue: 0.1937 time to fit residues: 90.6784 Evaluate side-chains 213 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 30.0000 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 0.5980 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 0.9980 overall best weight: 5.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 HIS ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN H 470 HIS I 337 HIS J 101 GLN J 177 ASN ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 HIS L 183 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.055178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.042031 restraints weight = 226778.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043125 restraints weight = 112976.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043825 restraints weight = 70495.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.044284 restraints weight = 50814.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.044572 restraints weight = 40756.328| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 38294 Z= 0.312 Angle : 0.658 10.418 52092 Z= 0.349 Chirality : 0.046 0.190 6253 Planarity : 0.004 0.061 6802 Dihedral : 4.484 44.817 5670 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.91 % Allowed : 7.51 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.12), residues: 5274 helix: 1.71 (0.11), residues: 2162 sheet: -1.11 (0.18), residues: 845 loop : -1.12 (0.14), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 234 TYR 0.034 0.002 TYR G 259 PHE 0.028 0.002 PHE Q 137 TRP 0.016 0.002 TRP N 135 HIS 0.006 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00695 (38294) covalent geometry : angle 0.65810 (52092) hydrogen bonds : bond 0.04341 ( 1903) hydrogen bonds : angle 4.89766 ( 5352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 138 ASN cc_start: 0.8822 (m110) cc_final: 0.8557 (m110) REVERT: F 130 MET cc_start: 0.8372 (ppp) cc_final: 0.8131 (ppp) REVERT: I 181 MET cc_start: 0.9011 (tpp) cc_final: 0.8696 (tpt) REVERT: J 107 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9514 (mm) REVERT: J 183 MET cc_start: 0.9523 (mmm) cc_final: 0.9272 (mtp) REVERT: K 153 MET cc_start: 0.8626 (tpp) cc_final: 0.8349 (tpp) REVERT: L 129 PHE cc_start: 0.9263 (m-80) cc_final: 0.9041 (m-80) REVERT: L 161 GLU cc_start: 0.8677 (mp0) cc_final: 0.8219 (mp0) REVERT: N 7 PHE cc_start: 0.8083 (m-10) cc_final: 0.7575 (m-10) REVERT: N 44 MET cc_start: 0.8091 (mmm) cc_final: 0.7844 (mmm) REVERT: N 130 PHE cc_start: 0.9327 (m-80) cc_final: 0.8602 (t80) REVERT: Q 22 ASN cc_start: 0.7895 (t0) cc_final: 0.7582 (t0) REVERT: Q 100 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8933 (tttt) REVERT: T 405 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5638 (pmm) outliers start: 30 outliers final: 16 residues processed: 215 average time/residue: 0.1987 time to fit residues: 74.8688 Evaluate side-chains 207 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain T residue 405 MET Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 421 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 523 optimal weight: 20.0000 chunk 479 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS E 236 GLN ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 HIS L 183 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.056350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.043112 restraints weight = 223121.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.044239 restraints weight = 110113.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044964 restraints weight = 68372.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.045437 restraints weight = 49170.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.045734 restraints weight = 39200.533| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 38294 Z= 0.137 Angle : 0.518 11.184 52092 Z= 0.280 Chirality : 0.043 0.165 6253 Planarity : 0.003 0.058 6802 Dihedral : 4.229 43.305 5670 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.91 % Allowed : 9.63 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.12), residues: 5274 helix: 2.03 (0.12), residues: 2140 sheet: -1.01 (0.18), residues: 833 loop : -0.95 (0.14), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 315 TYR 0.023 0.001 TYR G 259 PHE 0.031 0.001 PHE Q 137 TRP 0.010 0.001 TRP N 135 HIS 0.008 0.001 HIS L 183 Details of bonding type rmsd covalent geometry : bond 0.00300 (38294) covalent geometry : angle 0.51759 (52092) hydrogen bonds : bond 0.03561 ( 1903) hydrogen bonds : angle 4.45747 ( 5352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.8046 (m-80) cc_final: 0.7679 (m-10) REVERT: C 138 ASN cc_start: 0.8800 (m110) cc_final: 0.8539 (m110) REVERT: F 130 MET cc_start: 0.8369 (ppp) cc_final: 0.7723 (ppp) REVERT: I 181 MET cc_start: 0.8957 (tpp) cc_final: 0.8705 (tpp) REVERT: J 107 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9473 (mm) REVERT: J 183 MET cc_start: 0.9519 (mmm) cc_final: 0.9288 (mtp) REVERT: K 147 MET cc_start: 0.8801 (mmm) cc_final: 0.8549 (mmm) REVERT: K 153 MET cc_start: 0.8552 (tpp) cc_final: 0.8219 (tpp) REVERT: L 84 LYS cc_start: 0.9234 (ptmm) cc_final: 0.8640 (pptt) REVERT: L 86 MET cc_start: 0.8496 (ptm) cc_final: 0.7429 (pmm) REVERT: L 161 GLU cc_start: 0.8857 (mp0) cc_final: 0.8263 (mp0) REVERT: N 130 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8571 (t80) REVERT: Q 22 ASN cc_start: 0.7816 (t0) cc_final: 0.7472 (t0) REVERT: Q 100 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8866 (tttt) outliers start: 30 outliers final: 13 residues processed: 232 average time/residue: 0.2106 time to fit residues: 84.6816 Evaluate side-chains 214 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain H residue 273 MET Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain N residue 130 PHE Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 130 PHE Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 451 optimal weight: 10.0000 chunk 291 optimal weight: 7.9990 chunk 414 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 387 optimal weight: 8.9990 chunk 407 optimal weight: 7.9990 chunk 328 optimal weight: 7.9990 chunk 504 optimal weight: 10.0000 chunk 467 optimal weight: 5.9990 chunk 462 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 ASN H 234 GLN H 317 GLN J 304 HIS J 337 HIS ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.054690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.041603 restraints weight = 226827.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.042671 restraints weight = 114274.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.043364 restraints weight = 71694.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043805 restraints weight = 52077.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.044085 restraints weight = 41775.151| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 38294 Z= 0.317 Angle : 0.655 10.791 52092 Z= 0.346 Chirality : 0.046 0.236 6253 Planarity : 0.004 0.061 6802 Dihedral : 4.587 44.640 5670 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.82 % Allowed : 12.24 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 5274 helix: 1.76 (0.11), residues: 2136 sheet: -1.18 (0.18), residues: 841 loop : -1.16 (0.14), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 143 TYR 0.039 0.002 TYR G 259 PHE 0.038 0.002 PHE F 67 TRP 0.010 0.001 TRP S 451 HIS 0.006 0.001 HIS I 288 Details of bonding type rmsd covalent geometry : bond 0.00702 (38294) covalent geometry : angle 0.65524 (52092) hydrogen bonds : bond 0.04043 ( 1903) hydrogen bonds : angle 4.73948 ( 5352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 192 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8324 (ttt) REVERT: E 132 MET cc_start: 0.8974 (mmm) cc_final: 0.8655 (mmm) REVERT: F 130 MET cc_start: 0.8669 (ppp) cc_final: 0.8315 (ppp) REVERT: G 259 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7605 (m-10) REVERT: I 181 MET cc_start: 0.8949 (tpp) cc_final: 0.8663 (tpp) REVERT: J 107 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9486 (mm) REVERT: K 86 MET cc_start: 0.5602 (ppp) cc_final: 0.5348 (ppp) REVERT: K 153 MET cc_start: 0.8626 (tpp) cc_final: 0.8356 (tpp) REVERT: N 7 PHE cc_start: 0.8072 (m-10) cc_final: 0.7613 (m-10) REVERT: N 20 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7899 (tpt) REVERT: N 130 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8622 (t80) REVERT: Q 22 ASN cc_start: 0.7870 (t0) cc_final: 0.7557 (t0) REVERT: Q 100 LYS cc_start: 0.9198 (ttmt) cc_final: 0.8940 (tttt) outliers start: 60 outliers final: 33 residues processed: 235 average time/residue: 0.2038 time to fit residues: 84.7742 Evaluate side-chains 227 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 27 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 130 PHE Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain T residue 405 MET Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 101 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 362 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 chunk 531 optimal weight: 10.0000 chunk 378 optimal weight: 2.9990 chunk 458 optimal weight: 50.0000 chunk 530 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 332 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN H 234 GLN J 304 HIS J 337 HIS ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.056189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.042943 restraints weight = 221466.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.044087 restraints weight = 109735.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.044781 restraints weight = 68255.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.045259 restraints weight = 49061.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.045573 restraints weight = 39280.822| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 38294 Z= 0.122 Angle : 0.517 10.276 52092 Z= 0.278 Chirality : 0.043 0.182 6253 Planarity : 0.003 0.059 6802 Dihedral : 4.258 43.070 5670 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.48 % Allowed : 13.42 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 5274 helix: 2.12 (0.12), residues: 2133 sheet: -1.03 (0.18), residues: 820 loop : -0.99 (0.14), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 269 TYR 0.028 0.001 TYR G 259 PHE 0.029 0.001 PHE Q 137 TRP 0.013 0.001 TRP S 451 HIS 0.007 0.001 HIS L 183 Details of bonding type rmsd covalent geometry : bond 0.00263 (38294) covalent geometry : angle 0.51705 (52092) hydrogen bonds : bond 0.03266 ( 1903) hydrogen bonds : angle 4.31357 ( 5352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8264 (ttt) REVERT: B 93 MET cc_start: 0.8935 (tpp) cc_final: 0.8687 (mmt) REVERT: C 138 ASN cc_start: 0.8640 (m110) cc_final: 0.8405 (m-40) REVERT: C 203 MET cc_start: 0.9263 (mmm) cc_final: 0.8792 (tpp) REVERT: D 44 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: F 130 MET cc_start: 0.8607 (ppp) cc_final: 0.8001 (ppp) REVERT: I 181 MET cc_start: 0.8989 (tpp) cc_final: 0.8725 (tpp) REVERT: J 107 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9469 (mm) REVERT: K 147 MET cc_start: 0.8730 (mmm) cc_final: 0.8486 (mmm) REVERT: K 153 MET cc_start: 0.8491 (tpp) cc_final: 0.8230 (tpp) REVERT: L 86 MET cc_start: 0.8347 (ptm) cc_final: 0.7447 (pmm) REVERT: N 7 PHE cc_start: 0.8071 (m-10) cc_final: 0.7609 (m-10) REVERT: N 20 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7637 (tpt) REVERT: N 130 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8564 (t80) REVERT: Q 22 ASN cc_start: 0.7782 (t0) cc_final: 0.7468 (t0) REVERT: Q 100 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8857 (tttt) outliers start: 49 outliers final: 28 residues processed: 236 average time/residue: 0.1929 time to fit residues: 80.2847 Evaluate side-chains 228 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 273 MET Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 27 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 130 PHE Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain T residue 405 MET Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 412 optimal weight: 5.9990 chunk 391 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 404 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 406 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 433 optimal weight: 50.0000 chunk 108 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 GLN ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.056540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.043306 restraints weight = 222226.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.044457 restraints weight = 109451.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.045166 restraints weight = 67848.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.045643 restraints weight = 48669.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.045935 restraints weight = 38853.605| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38294 Z= 0.119 Angle : 0.503 11.977 52092 Z= 0.270 Chirality : 0.043 0.170 6253 Planarity : 0.003 0.058 6802 Dihedral : 4.079 42.131 5670 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.42 % Allowed : 14.02 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.12), residues: 5274 helix: 2.23 (0.12), residues: 2143 sheet: -0.93 (0.19), residues: 820 loop : -0.93 (0.14), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 269 TYR 0.023 0.001 TYR G 259 PHE 0.029 0.001 PHE Q 137 TRP 0.017 0.001 TRP Q 135 HIS 0.010 0.001 HIS K 183 Details of bonding type rmsd covalent geometry : bond 0.00257 (38294) covalent geometry : angle 0.50339 (52092) hydrogen bonds : bond 0.03037 ( 1903) hydrogen bonds : angle 4.14026 ( 5352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 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: A 164 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8244 (ttt) REVERT: B 93 MET cc_start: 0.8823 (tpp) cc_final: 0.8509 (mmt) REVERT: C 203 MET cc_start: 0.9284 (mmm) cc_final: 0.8781 (tpp) REVERT: D 44 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: F 130 MET cc_start: 0.8560 (ppp) cc_final: 0.7809 (ppp) REVERT: F 132 MET cc_start: 0.9094 (mmm) cc_final: 0.8607 (mmt) REVERT: I 181 MET cc_start: 0.9009 (tpp) cc_final: 0.8405 (tpp) REVERT: J 107 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9470 (mm) REVERT: K 147 MET cc_start: 0.8764 (mmm) cc_final: 0.8525 (mmm) REVERT: K 153 MET cc_start: 0.8562 (tpp) cc_final: 0.8360 (tpp) REVERT: L 65 TYR cc_start: 0.8623 (p90) cc_final: 0.8342 (p90) REVERT: L 86 MET cc_start: 0.8357 (ptm) cc_final: 0.7463 (pmm) REVERT: N 20 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7650 (tpt) REVERT: N 130 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8553 (t80) REVERT: Q 22 ASN cc_start: 0.7765 (t0) cc_final: 0.7449 (t0) REVERT: Q 100 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8879 (tttt) outliers start: 47 outliers final: 27 residues processed: 238 average time/residue: 0.2002 time to fit residues: 84.1880 Evaluate side-chains 230 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 27 TYR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 130 PHE Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain T residue 405 MET Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 441 optimal weight: 4.9990 chunk 385 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 197 optimal weight: 0.0980 chunk 228 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 399 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.056189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043011 restraints weight = 223140.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.044135 restraints weight = 110463.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.044866 restraints weight = 68433.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.045310 restraints weight = 49037.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.045603 restraints weight = 39195.104| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 38294 Z= 0.152 Angle : 0.525 11.936 52092 Z= 0.280 Chirality : 0.043 0.164 6253 Planarity : 0.003 0.058 6802 Dihedral : 4.074 42.092 5670 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.70 % Allowed : 14.05 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.12), residues: 5274 helix: 2.25 (0.12), residues: 2148 sheet: -0.93 (0.19), residues: 816 loop : -0.94 (0.14), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 143 TYR 0.026 0.001 TYR G 259 PHE 0.029 0.001 PHE Q 137 TRP 0.009 0.001 TRP S 451 HIS 0.005 0.001 HIS L 167 Details of bonding type rmsd covalent geometry : bond 0.00339 (38294) covalent geometry : angle 0.52541 (52092) hydrogen bonds : bond 0.03116 ( 1903) hydrogen bonds : angle 4.15163 ( 5352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8293 (ttt) REVERT: B 20 MET cc_start: 0.8852 (tmm) cc_final: 0.8589 (tmm) REVERT: C 203 MET cc_start: 0.9286 (mmm) cc_final: 0.8774 (tpp) REVERT: D 44 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: F 130 MET cc_start: 0.8537 (ppp) cc_final: 0.7757 (ppp) REVERT: F 132 MET cc_start: 0.9070 (mmm) cc_final: 0.8576 (mmt) REVERT: I 181 MET cc_start: 0.9104 (tpp) cc_final: 0.8753 (tpt) REVERT: J 107 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9477 (mm) REVERT: J 375 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8885 (p) REVERT: K 147 MET cc_start: 0.8767 (mmm) cc_final: 0.8528 (mmm) REVERT: L 86 MET cc_start: 0.8377 (ptm) cc_final: 0.7437 (pmm) REVERT: L 115 LYS cc_start: 0.9115 (tmtt) cc_final: 0.8356 (pttm) REVERT: L 168 LYS cc_start: 0.9445 (pttm) cc_final: 0.9129 (mmtt) REVERT: N 20 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7544 (tpt) REVERT: N 130 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8592 (t80) REVERT: Q 22 ASN cc_start: 0.7742 (t0) cc_final: 0.7420 (t0) REVERT: Q 100 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8880 (tttt) outliers start: 56 outliers final: 36 residues processed: 243 average time/residue: 0.2032 time to fit residues: 86.5148 Evaluate side-chains 237 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 27 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 130 PHE Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain T residue 405 MET Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 94 optimal weight: 1.9990 chunk 381 optimal weight: 1.9990 chunk 337 optimal weight: 2.9990 chunk 393 optimal weight: 6.9990 chunk 452 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 459 optimal weight: 0.4980 chunk 331 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.056519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.043320 restraints weight = 220739.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.044457 restraints weight = 109270.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.045190 restraints weight = 67822.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.045643 restraints weight = 48668.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.045928 restraints weight = 38862.301| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38294 Z= 0.128 Angle : 0.517 12.793 52092 Z= 0.276 Chirality : 0.043 0.189 6253 Planarity : 0.003 0.058 6802 Dihedral : 4.030 42.120 5670 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.42 % Allowed : 14.42 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 5274 helix: 2.29 (0.12), residues: 2146 sheet: -0.89 (0.19), residues: 816 loop : -0.91 (0.14), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 133 TYR 0.035 0.001 TYR L 65 PHE 0.039 0.001 PHE F 67 TRP 0.008 0.001 TRP H 476 HIS 0.004 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00283 (38294) covalent geometry : angle 0.51690 (52092) hydrogen bonds : bond 0.03010 ( 1903) hydrogen bonds : angle 4.09724 ( 5352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8247 (ttt) REVERT: C 203 MET cc_start: 0.9290 (mmm) cc_final: 0.8770 (tpp) REVERT: D 44 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: E 132 MET cc_start: 0.9008 (mmm) cc_final: 0.8346 (mmm) REVERT: F 67 PHE cc_start: 0.8485 (t80) cc_final: 0.8192 (m-80) REVERT: F 130 MET cc_start: 0.8536 (ppp) cc_final: 0.7803 (ppp) REVERT: F 132 MET cc_start: 0.9036 (mmm) cc_final: 0.8541 (mmt) REVERT: I 181 MET cc_start: 0.9102 (tpp) cc_final: 0.8864 (tpp) REVERT: J 107 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9470 (mm) REVERT: J 375 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8864 (p) REVERT: K 50 LYS cc_start: 0.9291 (mmmm) cc_final: 0.8686 (tptp) REVERT: K 147 MET cc_start: 0.8765 (mmm) cc_final: 0.8525 (mmm) REVERT: L 86 MET cc_start: 0.8383 (ptm) cc_final: 0.7435 (pmm) REVERT: L 115 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8440 (pttt) REVERT: L 129 PHE cc_start: 0.9365 (m-80) cc_final: 0.9128 (m-80) REVERT: L 161 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8698 (mp0) REVERT: N 7 PHE cc_start: 0.7991 (m-10) cc_final: 0.7541 (m-10) REVERT: N 20 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7444 (tpt) REVERT: N 130 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8594 (t80) REVERT: Q 22 ASN cc_start: 0.7732 (t0) cc_final: 0.7405 (t0) REVERT: Q 100 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8880 (tttt) outliers start: 47 outliers final: 37 residues processed: 240 average time/residue: 0.1896 time to fit residues: 80.1027 Evaluate side-chains 243 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 473 LEU Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 27 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 130 PHE Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain T residue 405 MET Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 425 optimal weight: 50.0000 chunk 163 optimal weight: 0.9990 chunk 103 optimal weight: 0.0670 chunk 99 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 475 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 386 optimal weight: 0.2980 chunk 43 optimal weight: 6.9990 chunk 410 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 431 ASN J 118 ASN ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.057129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.043880 restraints weight = 222568.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.045039 restraints weight = 108850.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045786 restraints weight = 66931.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.046266 restraints weight = 47810.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.046577 restraints weight = 38068.167| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 38294 Z= 0.105 Angle : 0.510 12.898 52092 Z= 0.271 Chirality : 0.043 0.181 6253 Planarity : 0.003 0.057 6802 Dihedral : 3.921 42.541 5670 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.21 % Allowed : 14.78 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 5274 helix: 2.38 (0.12), residues: 2140 sheet: -0.82 (0.19), residues: 827 loop : -0.86 (0.14), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 29 TYR 0.027 0.001 TYR B 83 PHE 0.031 0.001 PHE Q 137 TRP 0.007 0.001 TRP H 476 HIS 0.004 0.000 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00224 (38294) covalent geometry : angle 0.51018 (52092) hydrogen bonds : bond 0.02827 ( 1903) hydrogen bonds : angle 3.99354 ( 5352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 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: A 164 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8185 (ttt) REVERT: C 203 MET cc_start: 0.9279 (mmm) cc_final: 0.8769 (tpp) REVERT: E 1 MET cc_start: 0.8537 (tpt) cc_final: 0.8204 (tpt) REVERT: E 132 MET cc_start: 0.8989 (mmm) cc_final: 0.8497 (mmm) REVERT: F 130 MET cc_start: 0.8501 (ppp) cc_final: 0.8060 (ppp) REVERT: J 107 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9460 (mm) REVERT: J 375 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8791 (p) REVERT: K 50 LYS cc_start: 0.9273 (mmmm) cc_final: 0.8666 (tptp) REVERT: K 147 MET cc_start: 0.8690 (mmm) cc_final: 0.8449 (mmm) REVERT: L 100 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.6170 (m-80) REVERT: L 115 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8360 (pttt) REVERT: L 129 PHE cc_start: 0.9389 (m-80) cc_final: 0.9161 (m-80) REVERT: L 168 LYS cc_start: 0.9446 (pttm) cc_final: 0.9089 (mttm) REVERT: N 20 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7397 (tpt) REVERT: N 130 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8577 (t80) REVERT: Q 22 ASN cc_start: 0.7686 (t0) cc_final: 0.7404 (t0) REVERT: Q 100 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8859 (tttt) REVERT: Q 111 LEU cc_start: 0.9316 (mm) cc_final: 0.9116 (mm) outliers start: 40 outliers final: 26 residues processed: 238 average time/residue: 0.2037 time to fit residues: 84.8794 Evaluate side-chains 235 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 27 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 130 PHE Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain T residue 405 MET Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 433 optimal weight: 40.0000 chunk 244 optimal weight: 0.8980 chunk 474 optimal weight: 7.9990 chunk 311 optimal weight: 0.8980 chunk 446 optimal weight: 30.0000 chunk 463 optimal weight: 50.0000 chunk 78 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 459 optimal weight: 3.9990 chunk 329 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 431 ASN ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.056724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.043495 restraints weight = 221620.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.044641 restraints weight = 109287.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.045376 restraints weight = 67551.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.045851 restraints weight = 48364.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046163 restraints weight = 38560.791| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38294 Z= 0.132 Angle : 0.529 12.702 52092 Z= 0.280 Chirality : 0.043 0.189 6253 Planarity : 0.003 0.058 6802 Dihedral : 3.914 42.303 5670 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.21 % Allowed : 14.96 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.12), residues: 5274 helix: 2.44 (0.12), residues: 2133 sheet: -0.77 (0.19), residues: 798 loop : -0.87 (0.14), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 14 TYR 0.026 0.001 TYR L 65 PHE 0.031 0.001 PHE Q 137 TRP 0.007 0.001 TRP H 476 HIS 0.008 0.001 HIS L 183 Details of bonding type rmsd covalent geometry : bond 0.00292 (38294) covalent geometry : angle 0.52900 (52092) hydrogen bonds : bond 0.02902 ( 1903) hydrogen bonds : angle 4.02447 ( 5352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10548 Ramachandran restraints generated. 5274 Oldfield, 0 Emsley, 5274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8223 (ttt) REVERT: C 203 MET cc_start: 0.9276 (mmm) cc_final: 0.8755 (tpp) REVERT: E 1 MET cc_start: 0.8579 (tpt) cc_final: 0.8220 (tpt) REVERT: E 132 MET cc_start: 0.9026 (mmm) cc_final: 0.8547 (mmm) REVERT: F 130 MET cc_start: 0.8531 (ppp) cc_final: 0.7940 (ppp) REVERT: F 132 MET cc_start: 0.9077 (mmm) cc_final: 0.8550 (mmt) REVERT: J 107 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9475 (mm) REVERT: J 375 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8796 (p) REVERT: K 50 LYS cc_start: 0.9288 (mmmm) cc_final: 0.8694 (tptp) REVERT: K 147 MET cc_start: 0.8712 (mmm) cc_final: 0.8469 (mmm) REVERT: L 86 MET cc_start: 0.8455 (ptp) cc_final: 0.7692 (pmm) REVERT: L 100 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: L 115 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8337 (pttt) REVERT: L 168 LYS cc_start: 0.9452 (pttm) cc_final: 0.9126 (mttm) REVERT: N 20 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7410 (tpt) REVERT: N 130 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8609 (t80) REVERT: Q 22 ASN cc_start: 0.7733 (t0) cc_final: 0.7435 (t0) REVERT: Q 100 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8867 (tttt) outliers start: 40 outliers final: 29 residues processed: 231 average time/residue: 0.1990 time to fit residues: 80.9198 Evaluate side-chains 237 residues out of total 4682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 27 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 130 PHE Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain S residue 456 TRP Chi-restraints excluded: chain T residue 405 MET Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 68 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 295 optimal weight: 9.9990 chunk 239 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 371 optimal weight: 0.8980 chunk 273 optimal weight: 0.9980 chunk 396 optimal weight: 3.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 431 ASN ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.057505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.044310 restraints weight = 220855.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.045483 restraints weight = 108063.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.046225 restraints weight = 66526.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.046709 restraints weight = 47486.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.047026 restraints weight = 37741.699| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 38294 Z= 0.103 Angle : 0.519 12.980 52092 Z= 0.273 Chirality : 0.043 0.193 6253 Planarity : 0.003 0.058 6802 Dihedral : 3.831 42.724 5670 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.97 % Allowed : 15.51 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.12), residues: 5274 helix: 2.43 (0.12), residues: 2139 sheet: -0.74 (0.19), residues: 830 loop : -0.84 (0.14), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 14 TYR 0.023 0.001 TYR L 65 PHE 0.032 0.001 PHE Q 137 TRP 0.007 0.001 TRP H 476 HIS 0.004 0.000 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00219 (38294) covalent geometry : angle 0.51850 (52092) hydrogen bonds : bond 0.02721 ( 1903) hydrogen bonds : angle 3.92817 ( 5352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6797.23 seconds wall clock time: 117 minutes 52.81 seconds (7072.81 seconds total)