Starting phenix.real_space_refine on Fri Mar 6 22:40:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jn4_22401/03_2026/7jn4_22401.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jn4_22401/03_2026/7jn4_22401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jn4_22401/03_2026/7jn4_22401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jn4_22401/03_2026/7jn4_22401.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jn4_22401/03_2026/7jn4_22401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jn4_22401/03_2026/7jn4_22401.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 280 5.16 5 C 22504 2.51 5 N 6240 2.21 5 O 6688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s 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: 35712 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "C" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "E" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "G" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "I" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "K" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "M" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "O" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "P" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "L" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "M" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 9.11, per 1000 atoms: 0.26 Number of scatterers: 35712 At special positions: 0 Unit cell: (145.41, 145.41, 127.07, 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 280 16.00 O 6688 8.00 N 6240 7.00 C 22504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS C 247 " distance=2.06 Simple disulfide: pdb=" SG CYS A 449 " - pdb=" SG CYS A 459 " distance=2.03 Simple disulfide: pdb=" SG CYS C 449 " - pdb=" SG CYS C 459 " distance=2.03 Simple disulfide: pdb=" SG CYS E 247 " - pdb=" SG CYS G 247 " distance=2.06 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 459 " distance=2.03 Simple disulfide: pdb=" SG CYS G 449 " - pdb=" SG CYS G 459 " distance=2.03 Simple disulfide: pdb=" SG CYS I 247 " - pdb=" SG CYS K 247 " distance=2.06 Simple disulfide: pdb=" SG CYS I 449 " - pdb=" SG CYS I 459 " distance=2.03 Simple disulfide: pdb=" SG CYS K 449 " - pdb=" SG CYS K 459 " distance=2.03 Simple disulfide: pdb=" SG CYS M 247 " - pdb=" SG CYS O 247 " distance=2.06 Simple disulfide: pdb=" SG CYS M 449 " - pdb=" SG CYS M 459 " distance=2.03 Simple disulfide: pdb=" SG CYS O 449 " - pdb=" SG CYS O 459 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.2 seconds 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8272 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 32 sheets defined 45.2% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.577A pdb=" N PHE A 108 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.545A pdb=" N GLY A 126 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.592A pdb=" N LYS A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.515A pdb=" N GLY A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 removed outlier: 3.687A pdb=" N LEU A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.933A pdb=" N ILE A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 Processing helix chain 'A' and resid 337 through 351 removed outlier: 3.662A pdb=" N VAL A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 395 removed outlier: 3.581A pdb=" N GLU A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 433 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.859A pdb=" N LYS A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'B' and resid 22 through 36 removed outlier: 4.007A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 removed outlier: 3.858A pdb=" N ILE B 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 100 removed outlier: 4.057A pdb=" N VAL B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 60 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.575A pdb=" N PHE C 108 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 121 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.544A pdb=" N GLY C 126 " --> pdb=" O ASN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.595A pdb=" N LYS C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.513A pdb=" N GLY C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.684A pdb=" N LEU C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 220 " --> pdb=" O ASP C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 273 through 287 Processing helix chain 'C' and resid 297 through 303 removed outlier: 3.932A pdb=" N ILE C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 322 Processing helix chain 'C' and resid 337 through 351 removed outlier: 3.694A pdb=" N VAL C 341 " --> pdb=" O GLY C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 395 removed outlier: 3.577A pdb=" N GLU C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 433 Processing helix chain 'C' and resid 440 through 452 removed outlier: 3.862A pdb=" N LYS C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 461 removed outlier: 3.857A pdb=" N VAL C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 4.008A pdb=" N ASN D 36 " --> pdb=" O TYR D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 60 removed outlier: 3.858A pdb=" N ILE D 58 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 100 removed outlier: 4.050A pdb=" N VAL D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.576A pdb=" N PHE E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 121 Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.547A pdb=" N GLY E 126 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.594A pdb=" N LYS E 146 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 Processing helix chain 'E' and resid 181 through 196 removed outlier: 3.509A pdb=" N GLY E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY E 196 " --> pdb=" O CYS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 233 removed outlier: 3.685A pdb=" N LEU E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE E 220 " --> pdb=" O ASP E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 273 through 287 Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.929A pdb=" N ILE E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 322 Processing helix chain 'E' and resid 337 through 351 removed outlier: 3.660A pdb=" N VAL E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 386 through 395 removed outlier: 3.568A pdb=" N GLU E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 433 Processing helix chain 'E' and resid 440 through 452 removed outlier: 3.855A pdb=" N LYS E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 460 Processing helix chain 'F' and resid 22 through 36 removed outlier: 4.012A pdb=" N ASN F 36 " --> pdb=" O TYR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 60 removed outlier: 3.858A pdb=" N ILE F 58 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 100 removed outlier: 4.043A pdb=" N VAL F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 92 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 60 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.578A pdb=" N PHE G 108 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 123 through 127 removed outlier: 3.548A pdb=" N GLY G 126 " --> pdb=" O ASN G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 removed outlier: 3.596A pdb=" N LYS G 146 " --> pdb=" O PRO G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 163 Processing helix chain 'G' and resid 181 through 196 removed outlier: 3.514A pdb=" N GLY G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY G 196 " --> pdb=" O CYS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 233 removed outlier: 3.684A pdb=" N LEU G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 261 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 273 through 287 Processing helix chain 'G' and resid 297 through 303 removed outlier: 3.930A pdb=" N ILE G 301 " --> pdb=" O MET G 297 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG G 303 " --> pdb=" O ALA G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 Processing helix chain 'G' and resid 337 through 351 removed outlier: 3.690A pdb=" N VAL G 341 " --> pdb=" O GLY G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 361 Processing helix chain 'G' and resid 383 through 385 No H-bonds generated for 'chain 'G' and resid 383 through 385' Processing helix chain 'G' and resid 386 through 395 removed outlier: 3.568A pdb=" N GLU G 392 " --> pdb=" O PRO G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 433 Processing helix chain 'G' and resid 440 through 452 removed outlier: 3.866A pdb=" N LYS G 450 " --> pdb=" O ARG G 446 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TRP G 451 " --> pdb=" O SER G 447 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER G 452 " --> pdb=" O ALA G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 461 removed outlier: 3.859A pdb=" N VAL G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 36 removed outlier: 4.010A pdb=" N ASN H 36 " --> pdb=" O TYR H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 60 removed outlier: 3.857A pdb=" N ILE H 58 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 100 removed outlier: 4.035A pdb=" N VAL H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 60 Processing helix chain 'I' and resid 104 through 108 removed outlier: 3.578A pdb=" N PHE I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 121 Processing helix chain 'I' and resid 123 through 127 removed outlier: 3.546A pdb=" N GLY I 126 " --> pdb=" O ASN I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 146 removed outlier: 3.600A pdb=" N LYS I 146 " --> pdb=" O PRO I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 163 Processing helix chain 'I' and resid 181 through 196 removed outlier: 3.511A pdb=" N GLY I 195 " --> pdb=" O GLU I 191 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY I 196 " --> pdb=" O CYS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 233 removed outlier: 3.686A pdb=" N LEU I 219 " --> pdb=" O ARG I 215 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE I 220 " --> pdb=" O ASP I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 261 Processing helix chain 'I' and resid 269 through 273 Processing helix chain 'I' and resid 273 through 287 Processing helix chain 'I' and resid 297 through 303 removed outlier: 3.926A pdb=" N ILE I 301 " --> pdb=" O MET I 297 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG I 303 " --> pdb=" O ALA I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 322 Processing helix chain 'I' and resid 337 through 351 removed outlier: 3.702A pdb=" N VAL I 341 " --> pdb=" O GLY I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 361 Processing helix chain 'I' and resid 383 through 385 No H-bonds generated for 'chain 'I' and resid 383 through 385' Processing helix chain 'I' and resid 386 through 395 removed outlier: 3.581A pdb=" N GLU I 392 " --> pdb=" O PRO I 388 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 433 Processing helix chain 'I' and resid 440 through 452 removed outlier: 3.858A pdb=" N LYS I 450 " --> pdb=" O ARG I 446 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP I 451 " --> pdb=" O SER I 447 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER I 452 " --> pdb=" O ALA I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 460 Processing helix chain 'J' and resid 22 through 36 removed outlier: 4.011A pdb=" N ASN J 36 " --> pdb=" O TYR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 60 removed outlier: 3.858A pdb=" N ILE J 58 " --> pdb=" O GLU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 100 removed outlier: 4.042A pdb=" N VAL J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU J 92 " --> pdb=" O GLN J 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.576A pdb=" N PHE K 108 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 121 Processing helix chain 'K' and resid 123 through 127 removed outlier: 3.546A pdb=" N GLY K 126 " --> pdb=" O ASN K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 146 removed outlier: 3.594A pdb=" N LYS K 146 " --> pdb=" O PRO K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 163 Processing helix chain 'K' and resid 181 through 196 removed outlier: 3.514A pdb=" N GLY K 195 " --> pdb=" O GLU K 191 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY K 196 " --> pdb=" O CYS K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 233 removed outlier: 3.684A pdb=" N LEU K 219 " --> pdb=" O ARG K 215 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE K 220 " --> pdb=" O ASP K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 261 Processing helix chain 'K' and resid 269 through 273 Processing helix chain 'K' and resid 273 through 287 Processing helix chain 'K' and resid 297 through 303 removed outlier: 3.931A pdb=" N ILE K 301 " --> pdb=" O MET K 297 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG K 303 " --> pdb=" O ALA K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 322 Processing helix chain 'K' and resid 337 through 351 removed outlier: 3.667A pdb=" N VAL K 341 " --> pdb=" O GLY K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 361 Processing helix chain 'K' and resid 383 through 385 No H-bonds generated for 'chain 'K' and resid 383 through 385' Processing helix chain 'K' and resid 386 through 395 removed outlier: 3.571A pdb=" N GLU K 392 " --> pdb=" O PRO K 388 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 433 Processing helix chain 'K' and resid 440 through 452 removed outlier: 3.868A pdb=" N LYS K 450 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP K 451 " --> pdb=" O SER K 447 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER K 452 " --> pdb=" O ALA K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 461 removed outlier: 3.859A pdb=" N VAL K 461 " --> pdb=" O ALA K 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 36 removed outlier: 4.010A pdb=" N ASN L 36 " --> pdb=" O TYR L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 60 removed outlier: 3.856A pdb=" N ILE L 58 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 100 removed outlier: 4.032A pdb=" N VAL L 89 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU L 92 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL L 94 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 60 Processing helix chain 'M' and resid 104 through 108 removed outlier: 3.575A pdb=" N PHE M 108 " --> pdb=" O ILE M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 121 Processing helix chain 'M' and resid 123 through 127 removed outlier: 3.539A pdb=" N GLY M 126 " --> pdb=" O ASN M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 146 removed outlier: 3.596A pdb=" N LYS M 146 " --> pdb=" O PRO M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 Processing helix chain 'M' and resid 181 through 196 removed outlier: 3.515A pdb=" N GLY M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY M 196 " --> pdb=" O CYS M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 233 removed outlier: 3.686A pdb=" N LEU M 219 " --> pdb=" O ARG M 215 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE M 220 " --> pdb=" O ASP M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 261 Processing helix chain 'M' and resid 269 through 273 Processing helix chain 'M' and resid 273 through 287 Processing helix chain 'M' and resid 297 through 303 removed outlier: 3.929A pdb=" N ILE M 301 " --> pdb=" O MET M 297 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG M 303 " --> pdb=" O ALA M 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 322 Processing helix chain 'M' and resid 337 through 351 removed outlier: 3.695A pdb=" N VAL M 341 " --> pdb=" O GLY M 337 " (cutoff:3.500A) Processing helix chain 'M' and resid 357 through 361 Processing helix chain 'M' and resid 383 through 385 No H-bonds generated for 'chain 'M' and resid 383 through 385' Processing helix chain 'M' and resid 386 through 395 removed outlier: 3.583A pdb=" N GLU M 392 " --> pdb=" O PRO M 388 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 433 Processing helix chain 'M' and resid 440 through 452 removed outlier: 3.855A pdb=" N LYS M 450 " --> pdb=" O ARG M 446 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP M 451 " --> pdb=" O SER M 447 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER M 452 " --> pdb=" O ALA M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 452 through 461 removed outlier: 3.827A pdb=" N VAL M 461 " --> pdb=" O ALA M 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 36 removed outlier: 4.010A pdb=" N ASN N 36 " --> pdb=" O TYR N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 60 removed outlier: 3.860A pdb=" N ILE N 58 " --> pdb=" O GLU N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 removed outlier: 4.049A pdb=" N VAL N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU N 92 " --> pdb=" O GLN N 88 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL N 94 " --> pdb=" O LEU N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 60 Processing helix chain 'O' and resid 104 through 108 removed outlier: 3.575A pdb=" N PHE O 108 " --> pdb=" O ILE O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'O' and resid 123 through 127 removed outlier: 3.544A pdb=" N GLY O 126 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 146 removed outlier: 3.592A pdb=" N LYS O 146 " --> pdb=" O PRO O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 163 Processing helix chain 'O' and resid 181 through 196 removed outlier: 3.513A pdb=" N GLY O 195 " --> pdb=" O GLU O 191 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY O 196 " --> pdb=" O CYS O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 233 removed outlier: 3.684A pdb=" N LEU O 219 " --> pdb=" O ARG O 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE O 220 " --> pdb=" O ASP O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 246 through 261 Processing helix chain 'O' and resid 269 through 273 Processing helix chain 'O' and resid 273 through 287 Processing helix chain 'O' and resid 297 through 303 removed outlier: 3.925A pdb=" N ILE O 301 " --> pdb=" O MET O 297 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG O 303 " --> pdb=" O ALA O 299 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 322 Processing helix chain 'O' and resid 337 through 351 removed outlier: 3.679A pdb=" N VAL O 341 " --> pdb=" O GLY O 337 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 361 Processing helix chain 'O' and resid 383 through 385 No H-bonds generated for 'chain 'O' and resid 383 through 385' Processing helix chain 'O' and resid 386 through 395 removed outlier: 3.585A pdb=" N GLU O 392 " --> pdb=" O PRO O 388 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 433 Processing helix chain 'O' and resid 440 through 452 removed outlier: 3.866A pdb=" N LYS O 450 " --> pdb=" O ARG O 446 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP O 451 " --> pdb=" O SER O 447 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER O 452 " --> pdb=" O ALA O 448 " (cutoff:3.500A) Processing helix chain 'O' and resid 452 through 460 Processing helix chain 'P' and resid 22 through 36 removed outlier: 4.008A pdb=" N ASN P 36 " --> pdb=" O TYR P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 60 removed outlier: 3.856A pdb=" N ILE P 58 " --> pdb=" O GLU P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 100 removed outlier: 4.038A pdb=" N VAL P 89 " --> pdb=" O ASP P 85 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU P 92 " --> pdb=" O GLN P 88 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL P 94 " --> pdb=" O LEU P 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.569A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLY A 308 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 133 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 removed outlier: 6.279A pdb=" N LEU A 326 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N SER A 379 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N HIS A 294 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ASN A 241 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'B' and resid 74 through 76 removed outlier: 4.496A pdb=" N LEU B 42 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL B 105 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU B 122 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 107 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY B 120 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 109 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 89 removed outlier: 5.574A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N GLY C 308 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU C 133 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 171 removed outlier: 6.279A pdb=" N LEU C 326 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N SER C 379 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE C 265 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS C 294 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS C 267 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N HIS C 238 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR C 200 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASN C 241 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AA8, first strand: chain 'D' and resid 74 through 76 removed outlier: 4.499A pdb=" N LEU D 42 " --> pdb=" O TRP D 76 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL D 105 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU D 122 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 107 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY D 120 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA D 109 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 89 removed outlier: 5.571A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLY E 308 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU E 133 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 171 removed outlier: 6.278A pdb=" N LEU E 326 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER E 379 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE E 265 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS E 294 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS E 267 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N HIS E 238 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET E 266 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU E 240 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP E 268 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR E 200 " --> pdb=" O TYR E 239 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ASN E 241 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'F' and resid 74 through 76 removed outlier: 4.503A pdb=" N LEU F 42 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL F 105 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU F 122 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU F 107 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY F 120 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA F 109 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 83 through 89 removed outlier: 5.576A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N GLY G 308 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU G 133 " --> pdb=" O GLY G 308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 171 removed outlier: 6.272A pdb=" N LEU G 326 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER G 379 " --> pdb=" O LEU G 326 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE G 265 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS G 294 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS G 267 " --> pdb=" O HIS G 294 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N HIS G 238 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N MET G 266 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP G 268 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR G 200 " --> pdb=" O TYR G 239 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASN G 241 " --> pdb=" O THR G 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'H' and resid 74 through 76 removed outlier: 4.503A pdb=" N LEU H 42 " --> pdb=" O TRP H 76 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL H 105 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU H 122 " --> pdb=" O VAL H 105 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU H 107 " --> pdb=" O GLY H 120 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY H 120 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA H 109 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 83 through 89 removed outlier: 5.576A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP I 86 " --> pdb=" O TYR I 100 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU I 37 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU I 138 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA I 39 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLY I 308 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU I 133 " --> pdb=" O GLY I 308 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 169 through 171 removed outlier: 6.279A pdb=" N LEU I 326 " --> pdb=" O VAL I 377 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER I 379 " --> pdb=" O LEU I 326 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE I 265 " --> pdb=" O HIS I 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS I 294 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS I 267 " --> pdb=" O HIS I 294 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS I 238 " --> pdb=" O ILE I 264 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N MET I 266 " --> pdb=" O HIS I 238 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU I 240 " --> pdb=" O MET I 266 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ASP I 268 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR I 200 " --> pdb=" O TYR I 239 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ASN I 241 " --> pdb=" O THR I 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 353 through 354 Processing sheet with id=AC2, first strand: chain 'J' and resid 74 through 76 removed outlier: 4.498A pdb=" N LEU J 42 " --> pdb=" O TRP J 76 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL J 105 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU J 122 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU J 107 " --> pdb=" O GLY J 120 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY J 120 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA J 109 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 83 through 89 removed outlier: 5.573A pdb=" N CYS K 84 " --> pdb=" O ALA K 102 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA K 102 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP K 86 " --> pdb=" O TYR K 100 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU K 37 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU K 138 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA K 39 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N GLY K 308 " --> pdb=" O ARG K 131 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU K 133 " --> pdb=" O GLY K 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 169 through 171 removed outlier: 6.272A pdb=" N LEU K 326 " --> pdb=" O VAL K 377 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER K 379 " --> pdb=" O LEU K 326 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE K 265 " --> pdb=" O HIS K 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS K 294 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS K 267 " --> pdb=" O HIS K 294 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N HIS K 238 " --> pdb=" O ILE K 264 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET K 266 " --> pdb=" O HIS K 238 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU K 240 " --> pdb=" O MET K 266 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP K 268 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR K 200 " --> pdb=" O TYR K 239 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASN K 241 " --> pdb=" O THR K 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 353 through 354 Processing sheet with id=AC6, first strand: chain 'L' and resid 74 through 76 removed outlier: 4.501A pdb=" N LEU L 42 " --> pdb=" O TRP L 76 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL L 105 " --> pdb=" O LEU L 122 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU L 122 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU L 107 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY L 120 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA L 109 " --> pdb=" O ILE L 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 83 through 89 removed outlier: 5.571A pdb=" N CYS M 84 " --> pdb=" O ALA M 102 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA M 102 " --> pdb=" O CYS M 84 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP M 86 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU M 37 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU M 138 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA M 39 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N GLY M 308 " --> pdb=" O ARG M 131 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU M 133 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 169 through 171 removed outlier: 6.280A pdb=" N LEU M 326 " --> pdb=" O VAL M 377 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N SER M 379 " --> pdb=" O LEU M 326 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE M 265 " --> pdb=" O HIS M 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS M 294 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS M 267 " --> pdb=" O HIS M 294 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N HIS M 238 " --> pdb=" O ILE M 264 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET M 266 " --> pdb=" O HIS M 238 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU M 240 " --> pdb=" O MET M 266 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASP M 268 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR M 200 " --> pdb=" O TYR M 239 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ASN M 241 " --> pdb=" O THR M 200 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 353 through 354 Processing sheet with id=AD1, first strand: chain 'N' and resid 74 through 76 removed outlier: 4.505A pdb=" N LEU N 42 " --> pdb=" O TRP N 76 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL N 105 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU N 122 " --> pdb=" O VAL N 105 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU N 107 " --> pdb=" O GLY N 120 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY N 120 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA N 109 " --> pdb=" O ILE N 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 83 through 89 removed outlier: 5.570A pdb=" N CYS O 84 " --> pdb=" O ALA O 102 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA O 102 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP O 86 " --> pdb=" O TYR O 100 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU O 37 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU O 138 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA O 39 " --> pdb=" O GLU O 136 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N GLY O 308 " --> pdb=" O ARG O 131 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU O 133 " --> pdb=" O GLY O 308 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 169 through 171 removed outlier: 6.273A pdb=" N LEU O 326 " --> pdb=" O VAL O 377 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER O 379 " --> pdb=" O LEU O 326 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE O 265 " --> pdb=" O HIS O 292 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N HIS O 294 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N HIS O 267 " --> pdb=" O HIS O 294 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS O 238 " --> pdb=" O ILE O 264 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N MET O 266 " --> pdb=" O HIS O 238 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU O 240 " --> pdb=" O MET O 266 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ASP O 268 " --> pdb=" O LEU O 240 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR O 200 " --> pdb=" O TYR O 239 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ASN O 241 " --> pdb=" O THR O 200 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 353 through 354 Processing sheet with id=AD5, first strand: chain 'P' and resid 74 through 76 removed outlier: 4.495A pdb=" N LEU P 42 " --> pdb=" O TRP P 76 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL P 105 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU P 122 " --> pdb=" O VAL P 105 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU P 107 " --> pdb=" O GLY P 120 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY P 120 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA P 109 " --> pdb=" O ILE P 118 " (cutoff:3.500A) 1496 hydrogen bonds defined for protein. 4152 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: 7.58 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11163 1.33 - 1.46: 9348 1.46 - 1.59: 15401 1.59 - 1.72: 0 1.72 - 1.84: 440 Bond restraints: 36352 Sorted by residual: bond pdb=" CB ARG O 194 " pdb=" CG ARG O 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.37e+01 bond pdb=" CB ARG I 194 " pdb=" CG ARG I 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.37e+01 bond pdb=" CB ARG K 194 " pdb=" CG ARG K 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.36e+01 bond pdb=" CB ARG E 194 " pdb=" CG ARG E 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.36e+01 bond pdb=" CB ARG A 194 " pdb=" CG ARG A 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.36e+01 ... (remaining 36347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 46358 2.31 - 4.62: 2382 4.62 - 6.94: 404 6.94 - 9.25: 88 9.25 - 11.56: 24 Bond angle restraints: 49256 Sorted by residual: angle pdb=" N GLU H 13 " pdb=" CA GLU H 13 " pdb=" C GLU H 13 " ideal model delta sigma weight residual 111.07 121.15 -10.08 1.07e+00 8.73e-01 8.88e+01 angle pdb=" N GLU L 13 " pdb=" CA GLU L 13 " pdb=" C GLU L 13 " ideal model delta sigma weight residual 111.07 121.12 -10.05 1.07e+00 8.73e-01 8.82e+01 angle pdb=" N GLU B 13 " pdb=" CA GLU B 13 " pdb=" C GLU B 13 " ideal model delta sigma weight residual 111.07 121.11 -10.04 1.07e+00 8.73e-01 8.81e+01 angle pdb=" N GLU N 13 " pdb=" CA GLU N 13 " pdb=" C GLU N 13 " ideal model delta sigma weight residual 111.07 121.11 -10.04 1.07e+00 8.73e-01 8.81e+01 angle pdb=" N GLU J 13 " pdb=" CA GLU J 13 " pdb=" C GLU J 13 " ideal model delta sigma weight residual 111.07 121.08 -10.01 1.07e+00 8.73e-01 8.76e+01 ... (remaining 49251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 20001 14.26 - 28.53: 1312 28.53 - 42.79: 194 42.79 - 57.05: 73 57.05 - 71.32: 48 Dihedral angle restraints: 21628 sinusoidal: 8660 harmonic: 12968 Sorted by residual: dihedral pdb=" N LYS M 175 " pdb=" C LYS M 175 " pdb=" CA LYS M 175 " pdb=" CB LYS M 175 " ideal model delta harmonic sigma weight residual 122.80 138.27 -15.47 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" N LYS K 175 " pdb=" C LYS K 175 " pdb=" CA LYS K 175 " pdb=" CB LYS K 175 " ideal model delta harmonic sigma weight residual 122.80 138.20 -15.40 0 2.50e+00 1.60e-01 3.80e+01 dihedral pdb=" N LYS A 175 " pdb=" C LYS A 175 " pdb=" CA LYS A 175 " pdb=" CB LYS A 175 " ideal model delta harmonic sigma weight residual 122.80 138.20 -15.40 0 2.50e+00 1.60e-01 3.80e+01 ... (remaining 21625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 5049 0.154 - 0.309: 142 0.309 - 0.463: 9 0.463 - 0.618: 0 0.618 - 0.772: 8 Chirality restraints: 5208 Sorted by residual: chirality pdb=" CA LYS M 175 " pdb=" N LYS M 175 " pdb=" C LYS M 175 " pdb=" CB LYS M 175 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" CA LYS A 175 " pdb=" N LYS A 175 " pdb=" C LYS A 175 " pdb=" CB LYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA LYS K 175 " pdb=" N LYS K 175 " pdb=" C LYS K 175 " pdb=" CB LYS K 175 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 5205 not shown) Planarity restraints: 6464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE O 148 " 0.021 2.00e-02 2.50e+03 2.59e-02 1.18e+01 pdb=" CG PHE O 148 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE O 148 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE O 148 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE O 148 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE O 148 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE O 148 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 148 " 0.021 2.00e-02 2.50e+03 2.59e-02 1.17e+01 pdb=" CG PHE A 148 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 148 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 148 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 148 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 148 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 148 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 148 " -0.020 2.00e-02 2.50e+03 2.58e-02 1.17e+01 pdb=" CG PHE K 148 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE K 148 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE K 148 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE K 148 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE K 148 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE K 148 " -0.003 2.00e-02 2.50e+03 ... (remaining 6461 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7288 2.76 - 3.30: 31153 3.30 - 3.83: 62925 3.83 - 4.37: 81936 4.37 - 4.90: 133146 Nonbonded interactions: 316448 Sorted by model distance: nonbonded pdb=" OD2 ASP M 216 " pdb=" O HOH M 501 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP C 216 " pdb=" O HOH C 501 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP A 216 " pdb=" O HOH A 501 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP G 216 " pdb=" O HOH G 501 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP O 216 " pdb=" O HOH O 501 " model vdw 2.229 3.040 ... (remaining 316443 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 31.980 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.013 0.111 36364 Z= 0.540 Angle : 1.228 11.559 49280 Z= 0.698 Chirality : 0.076 0.772 5208 Planarity : 0.009 0.063 6464 Dihedral : 10.930 71.315 13320 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.33 % Allowed : 3.19 % Favored : 95.48 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.09), residues: 4448 helix: -3.73 (0.07), residues: 1656 sheet: -1.59 (0.17), residues: 760 loop : -1.69 (0.11), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG K 253 TYR 0.042 0.006 TYR J 17 PHE 0.057 0.007 PHE O 148 TRP 0.028 0.005 TRP P 73 HIS 0.019 0.005 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.01261 (36352) covalent geometry : angle 1.22134 (49256) SS BOND : bond 0.01759 ( 12) SS BOND : angle 6.05400 ( 24) hydrogen bonds : bond 0.28086 ( 1496) hydrogen bonds : angle 9.72828 ( 4152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 718 time to evaluate : 1.296 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 81 LYS cc_start: 0.8575 (pttt) cc_final: 0.8337 (pttt) REVERT: A 340 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7242 (tp30) REVERT: B 77 LYS cc_start: 0.8924 (mttt) cc_final: 0.8684 (mttt) REVERT: B 92 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8024 (mm-30) REVERT: B 114 LYS cc_start: 0.6297 (ttmt) cc_final: 0.5865 (ttpt) REVERT: B 133 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8125 (mm110) REVERT: C 81 LYS cc_start: 0.8639 (pttt) cc_final: 0.8424 (pttt) REVERT: C 340 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7244 (tp30) REVERT: C 349 MET cc_start: 0.8776 (mtp) cc_final: 0.8573 (mtm) REVERT: D 92 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8009 (mm-30) REVERT: D 114 LYS cc_start: 0.6073 (ttmt) cc_final: 0.5726 (ttpt) REVERT: D 133 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8073 (mm110) REVERT: E 81 LYS cc_start: 0.8619 (pttt) cc_final: 0.8411 (pttt) REVERT: E 340 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7259 (tp30) REVERT: E 349 MET cc_start: 0.8773 (mtp) cc_final: 0.8568 (mtm) REVERT: F 92 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8027 (mm-30) REVERT: F 114 LYS cc_start: 0.6108 (ttmt) cc_final: 0.5785 (ttpt) REVERT: F 133 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8078 (mm110) REVERT: G 340 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7234 (tp30) REVERT: G 349 MET cc_start: 0.8777 (mtp) cc_final: 0.8571 (mtm) REVERT: H 92 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8002 (mm-30) REVERT: H 114 LYS cc_start: 0.6148 (ttmt) cc_final: 0.5804 (ttpt) REVERT: I 81 LYS cc_start: 0.8639 (pttt) cc_final: 0.8428 (pttt) REVERT: I 340 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7213 (tp30) REVERT: J 92 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8004 (mm-30) REVERT: J 114 LYS cc_start: 0.6126 (ttmt) cc_final: 0.5809 (ttpt) REVERT: J 133 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8054 (mm110) REVERT: K 340 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7262 (tp30) REVERT: K 349 MET cc_start: 0.8777 (mtp) cc_final: 0.8572 (mtm) REVERT: L 77 LYS cc_start: 0.8877 (mttt) cc_final: 0.8630 (mttt) REVERT: L 92 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8014 (mm-30) REVERT: L 114 LYS cc_start: 0.6104 (ttmt) cc_final: 0.5799 (ttpt) REVERT: M 340 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7245 (tp30) REVERT: M 349 MET cc_start: 0.8772 (mtp) cc_final: 0.8572 (mtm) REVERT: N 92 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8042 (mm-30) REVERT: N 114 LYS cc_start: 0.6072 (ttmt) cc_final: 0.5710 (ttpt) REVERT: N 133 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8067 (mm110) REVERT: O 81 LYS cc_start: 0.8580 (pttt) cc_final: 0.8334 (pttt) REVERT: O 340 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7188 (tp30) REVERT: P 92 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8005 (mm-30) REVERT: P 114 LYS cc_start: 0.6414 (ttmt) cc_final: 0.5990 (ttpt) outliers start: 41 outliers final: 16 residues processed: 750 average time/residue: 0.8334 time to fit residues: 728.3268 Evaluate side-chains 653 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 637 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0570 chunk 401 optimal weight: 0.2980 chunk 424 optimal weight: 5.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 163 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 238 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 304 GLN B 9 ASN C 96 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS C 163 ASN C 207 ASN C 229 GLN C 238 HIS C 241 ASN C 277 ASN C 304 GLN ** D 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS E 163 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN E 238 HIS ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN E 304 GLN F 9 ASN ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS G 163 ASN G 207 ASN G 229 GLN G 238 HIS G 241 ASN G 277 ASN G 304 GLN H 9 ASN I 96 GLN I 153 HIS I 163 ASN I 207 ASN I 229 GLN I 238 HIS I 241 ASN I 277 ASN I 304 GLN J 9 ASN K 153 HIS K 163 ASN K 207 ASN K 229 GLN K 238 HIS K 241 ASN K 277 ASN K 304 GLN L 9 ASN M 96 GLN M 153 HIS M 163 ASN M 207 ASN M 229 GLN M 238 HIS M 241 ASN M 277 ASN M 304 GLN N 9 ASN O 96 GLN O 153 HIS O 163 ASN O 207 ASN O 229 GLN O 238 HIS O 241 ASN O 277 ASN O 304 GLN P 9 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.173482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136686 restraints weight = 33843.654| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.54 r_work: 0.3234 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 36364 Z= 0.123 Angle : 0.620 9.040 49280 Z= 0.321 Chirality : 0.043 0.163 5208 Planarity : 0.005 0.052 6464 Dihedral : 6.710 58.316 5048 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.88 % Allowed : 7.92 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.11), residues: 4448 helix: -0.91 (0.11), residues: 1648 sheet: -1.07 (0.17), residues: 808 loop : -1.08 (0.12), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 187 TYR 0.013 0.001 TYR H 67 PHE 0.037 0.002 PHE G 345 TRP 0.014 0.001 TRP B 73 HIS 0.004 0.001 HIS I 238 Details of bonding type rmsd covalent geometry : bond 0.00266 (36352) covalent geometry : angle 0.61475 (49256) SS BOND : bond 0.00947 ( 12) SS BOND : angle 3.73605 ( 24) hydrogen bonds : bond 0.03985 ( 1496) hydrogen bonds : angle 5.25403 ( 4152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 686 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8451 (mmmt) cc_final: 0.7839 (mptt) REVERT: A 158 GLU cc_start: 0.8722 (tt0) cc_final: 0.8506 (tt0) REVERT: A 205 ASN cc_start: 0.8355 (p0) cc_final: 0.8107 (p0) REVERT: A 305 ARG cc_start: 0.8472 (ttt-90) cc_final: 0.7775 (ttp80) REVERT: B 111 ASP cc_start: 0.7257 (t0) cc_final: 0.6977 (t0) REVERT: B 133 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8119 (mm110) REVERT: C 52 GLU cc_start: 0.7814 (tp30) cc_final: 0.7310 (tm-30) REVERT: C 128 LYS cc_start: 0.8446 (mmmt) cc_final: 0.7809 (mppt) REVERT: C 205 ASN cc_start: 0.8550 (p0) cc_final: 0.8333 (p0) REVERT: C 305 ARG cc_start: 0.8438 (ttt-90) cc_final: 0.7817 (ttp80) REVERT: C 349 MET cc_start: 0.8729 (mtp) cc_final: 0.8333 (mtm) REVERT: D 111 ASP cc_start: 0.7171 (t0) cc_final: 0.6882 (t0) REVERT: E 128 LYS cc_start: 0.8512 (mmmt) cc_final: 0.7834 (mptt) REVERT: E 158 GLU cc_start: 0.8696 (tt0) cc_final: 0.8481 (tt0) REVERT: E 205 ASN cc_start: 0.8542 (p0) cc_final: 0.8219 (p0) REVERT: E 349 MET cc_start: 0.8729 (mtp) cc_final: 0.8339 (mtm) REVERT: E 392 GLU cc_start: 0.8452 (tt0) cc_final: 0.8026 (tp30) REVERT: F 111 ASP cc_start: 0.7208 (t0) cc_final: 0.6891 (t0) REVERT: F 114 LYS cc_start: 0.6018 (ttmt) cc_final: 0.5813 (ttpt) REVERT: G 79 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7884 (mtm-85) REVERT: G 128 LYS cc_start: 0.8523 (mmmt) cc_final: 0.7842 (mppt) REVERT: G 158 GLU cc_start: 0.8719 (tt0) cc_final: 0.8498 (tt0) REVERT: G 205 ASN cc_start: 0.8571 (p0) cc_final: 0.8346 (p0) REVERT: G 349 MET cc_start: 0.8726 (mtp) cc_final: 0.8333 (mtm) REVERT: G 392 GLU cc_start: 0.8422 (tt0) cc_final: 0.8014 (tp30) REVERT: H 87 MET cc_start: 0.7785 (pmm) cc_final: 0.7240 (pmm) REVERT: H 111 ASP cc_start: 0.7291 (t0) cc_final: 0.7022 (t0) REVERT: H 114 LYS cc_start: 0.6098 (ttmt) cc_final: 0.5844 (ttpt) REVERT: I 96 GLN cc_start: 0.9125 (mt0) cc_final: 0.8925 (mt0) REVERT: I 128 LYS cc_start: 0.8516 (mmmt) cc_final: 0.7835 (mppt) REVERT: I 158 GLU cc_start: 0.8716 (tt0) cc_final: 0.8504 (tt0) REVERT: I 305 ARG cc_start: 0.8451 (ttt-90) cc_final: 0.8203 (ttt180) REVERT: J 111 ASP cc_start: 0.7228 (t0) cc_final: 0.6902 (t0) REVERT: K 158 GLU cc_start: 0.8711 (tt0) cc_final: 0.8492 (tt0) REVERT: K 205 ASN cc_start: 0.8567 (p0) cc_final: 0.8262 (p0) REVERT: K 349 MET cc_start: 0.8727 (mtp) cc_final: 0.8333 (mtm) REVERT: L 92 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7975 (mm-30) REVERT: L 111 ASP cc_start: 0.7202 (t0) cc_final: 0.6914 (t0) REVERT: L 114 LYS cc_start: 0.6063 (ttmt) cc_final: 0.5802 (ttpt) REVERT: M 52 GLU cc_start: 0.7751 (tp30) cc_final: 0.7339 (mm-30) REVERT: M 79 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7890 (mtm-85) REVERT: M 158 GLU cc_start: 0.8696 (tt0) cc_final: 0.8483 (tt0) REVERT: M 203 ASP cc_start: 0.8290 (t70) cc_final: 0.8076 (t70) REVERT: M 205 ASN cc_start: 0.8544 (p0) cc_final: 0.8227 (p0) REVERT: M 305 ARG cc_start: 0.8451 (ttt-90) cc_final: 0.7825 (ttp80) REVERT: M 349 MET cc_start: 0.8733 (mtp) cc_final: 0.8344 (mtm) REVERT: N 111 ASP cc_start: 0.7275 (t0) cc_final: 0.7028 (t0) REVERT: O 52 GLU cc_start: 0.7770 (tp30) cc_final: 0.7474 (mm-30) REVERT: O 128 LYS cc_start: 0.8461 (mmmt) cc_final: 0.7830 (mptt) REVERT: O 158 GLU cc_start: 0.8712 (tt0) cc_final: 0.8494 (tt0) REVERT: O 203 ASP cc_start: 0.8296 (t70) cc_final: 0.8091 (t70) REVERT: O 205 ASN cc_start: 0.8538 (p0) cc_final: 0.8233 (p0) REVERT: O 305 ARG cc_start: 0.8469 (ttt-90) cc_final: 0.7855 (ttp80) REVERT: P 111 ASP cc_start: 0.7254 (t0) cc_final: 0.6950 (t0) REVERT: P 114 LYS cc_start: 0.5982 (ttmt) cc_final: 0.5773 (ttpt) REVERT: P 133 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8095 (mm110) outliers start: 61 outliers final: 20 residues processed: 720 average time/residue: 0.8377 time to fit residues: 701.7745 Evaluate side-chains 638 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 618 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 440 GLU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 440 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 420 optimal weight: 1.9990 chunk 437 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 115 ASN A 153 HIS A 241 ASN A 277 ASN A 287 ASN A 420 ASN A 432 ASN B 29 GLN C 96 GLN C 153 HIS C 207 ASN C 277 ASN C 287 ASN C 432 ASN D 9 ASN D 29 GLN E 96 GLN E 115 ASN E 153 HIS E 241 ASN E 277 ASN E 287 ASN E 420 ASN E 432 ASN F 29 GLN G 96 GLN G 153 HIS G 207 ASN G 277 ASN G 287 ASN G 420 ASN G 432 ASN H 29 GLN H 133 GLN I 115 ASN I 153 HIS I 207 ASN I 277 ASN I 287 ASN I 420 ASN I 432 ASN J 29 GLN K 96 GLN K 115 ASN K 153 HIS K 207 ASN K 277 ASN K 287 ASN K 420 ASN K 432 ASN L 29 GLN M 96 GLN M 115 ASN M 153 HIS M 207 ASN M 277 ASN M 287 ASN M 420 ASN M 432 ASN N 29 GLN O 96 GLN O 115 ASN O 153 HIS O 207 ASN O 277 ASN O 287 ASN O 420 ASN O 432 ASN P 29 GLN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.165849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127159 restraints weight = 33317.983| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.67 r_work: 0.3064 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 36364 Z= 0.318 Angle : 0.763 9.859 49280 Z= 0.392 Chirality : 0.051 0.194 5208 Planarity : 0.006 0.052 6464 Dihedral : 6.795 56.253 5048 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.56 % Allowed : 9.34 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.11), residues: 4448 helix: 0.25 (0.12), residues: 1648 sheet: -0.86 (0.17), residues: 800 loop : -0.95 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 253 TYR 0.020 0.003 TYR O 226 PHE 0.035 0.004 PHE G 345 TRP 0.013 0.002 TRP J 73 HIS 0.009 0.003 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00761 (36352) covalent geometry : angle 0.75498 (49256) SS BOND : bond 0.01705 ( 12) SS BOND : angle 5.05160 ( 24) hydrogen bonds : bond 0.05237 ( 1496) hydrogen bonds : angle 5.10373 ( 4152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 610 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7863 (tp30) cc_final: 0.7328 (tm-30) REVERT: A 205 ASN cc_start: 0.8520 (p0) cc_final: 0.8225 (p0) REVERT: A 253 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8807 (mpt180) REVERT: A 305 ARG cc_start: 0.8555 (ttt-90) cc_final: 0.7970 (ttp80) REVERT: A 355 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8046 (tp30) REVERT: B 49 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.6876 (mtpt) REVERT: B 80 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7470 (mmt) REVERT: B 111 ASP cc_start: 0.7453 (t0) cc_final: 0.7085 (t0) REVERT: C 52 GLU cc_start: 0.7902 (tp30) cc_final: 0.7701 (tp30) REVERT: C 128 LYS cc_start: 0.8527 (mmmt) cc_final: 0.7901 (mptt) REVERT: C 205 ASN cc_start: 0.8524 (p0) cc_final: 0.8242 (p0) REVERT: C 253 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8800 (mpt180) REVERT: C 305 ARG cc_start: 0.8542 (ttt-90) cc_final: 0.7959 (ttp80) REVERT: C 339 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7280 (ttm170) REVERT: C 349 MET cc_start: 0.8920 (mtp) cc_final: 0.8591 (mtm) REVERT: D 49 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.6904 (mtpt) REVERT: D 80 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7508 (mmt) REVERT: D 111 ASP cc_start: 0.7540 (t0) cc_final: 0.7222 (t0) REVERT: E 52 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7427 (tm-30) REVERT: E 203 ASP cc_start: 0.8379 (t70) cc_final: 0.8170 (t0) REVERT: E 305 ARG cc_start: 0.8577 (ttt-90) cc_final: 0.7994 (ttp80) REVERT: E 339 ARG cc_start: 0.8079 (ttp-170) cc_final: 0.7287 (ttm170) REVERT: E 349 MET cc_start: 0.8929 (mtp) cc_final: 0.8607 (mtm) REVERT: E 355 GLU cc_start: 0.8237 (mm-30) cc_final: 0.8012 (tp30) REVERT: F 49 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.6949 (mtpt) REVERT: F 80 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7523 (mmt) REVERT: F 111 ASP cc_start: 0.7562 (t0) cc_final: 0.7286 (t0) REVERT: F 114 LYS cc_start: 0.6231 (ttmt) cc_final: 0.6029 (ttpt) REVERT: G 205 ASN cc_start: 0.8541 (p0) cc_final: 0.8209 (p0) REVERT: G 305 ARG cc_start: 0.8576 (ttt-90) cc_final: 0.7913 (ttp80) REVERT: G 349 MET cc_start: 0.8922 (mtp) cc_final: 0.8595 (mtm) REVERT: H 49 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.6904 (mtpt) REVERT: H 80 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7442 (mmt) REVERT: H 87 MET cc_start: 0.7900 (pmm) cc_final: 0.7269 (pmm) REVERT: H 111 ASP cc_start: 0.7554 (t0) cc_final: 0.7207 (t0) REVERT: H 114 LYS cc_start: 0.6204 (ttmt) cc_final: 0.5983 (ttpt) REVERT: H 133 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8024 (mm110) REVERT: I 52 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7430 (tm-30) REVERT: I 205 ASN cc_start: 0.8522 (p0) cc_final: 0.8237 (p0) REVERT: I 305 ARG cc_start: 0.8573 (ttt-90) cc_final: 0.8345 (ttt180) REVERT: J 49 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.6899 (mtpt) REVERT: J 80 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7501 (mmt) REVERT: J 111 ASP cc_start: 0.7568 (t0) cc_final: 0.7273 (t0) REVERT: K 203 ASP cc_start: 0.8387 (t70) cc_final: 0.8182 (t0) REVERT: K 305 ARG cc_start: 0.8581 (ttt-90) cc_final: 0.7916 (ttp80) REVERT: K 339 ARG cc_start: 0.8101 (ttp-170) cc_final: 0.7288 (ttm170) REVERT: K 349 MET cc_start: 0.8930 (mtp) cc_final: 0.8607 (mtm) REVERT: K 355 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8009 (tp30) REVERT: K 425 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8349 (mt-10) REVERT: L 49 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.6899 (mtpt) REVERT: L 80 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7468 (mmt) REVERT: L 111 ASP cc_start: 0.7544 (t0) cc_final: 0.7171 (t0) REVERT: L 114 LYS cc_start: 0.6173 (ttmt) cc_final: 0.5925 (ttpt) REVERT: M 52 GLU cc_start: 0.7717 (tp30) cc_final: 0.7274 (mm-30) REVERT: M 203 ASP cc_start: 0.8500 (t70) cc_final: 0.8292 (t70) REVERT: M 205 ASN cc_start: 0.8741 (p0) cc_final: 0.8389 (p0) REVERT: M 253 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8838 (mpt180) REVERT: M 305 ARG cc_start: 0.8563 (ttt-90) cc_final: 0.7971 (ttp80) REVERT: M 349 MET cc_start: 0.8920 (mtp) cc_final: 0.8591 (mtm) REVERT: N 49 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.6915 (mtpt) REVERT: N 80 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7521 (mmt) REVERT: N 111 ASP cc_start: 0.7478 (t0) cc_final: 0.7123 (t0) REVERT: O 52 GLU cc_start: 0.7808 (tp30) cc_final: 0.7458 (mm-30) REVERT: O 203 ASP cc_start: 0.8475 (t70) cc_final: 0.8266 (t70) REVERT: O 205 ASN cc_start: 0.8732 (p0) cc_final: 0.8378 (p0) REVERT: O 253 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8824 (mpt180) REVERT: O 305 ARG cc_start: 0.8578 (ttt-90) cc_final: 0.7997 (ttp80) REVERT: O 355 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8007 (tp30) REVERT: P 49 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.6895 (mtpt) REVERT: P 80 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7519 (mmt) REVERT: P 111 ASP cc_start: 0.7440 (t0) cc_final: 0.7156 (t0) REVERT: P 114 LYS cc_start: 0.6159 (ttmt) cc_final: 0.5956 (ttpt) outliers start: 86 outliers final: 40 residues processed: 664 average time/residue: 0.8647 time to fit residues: 664.8097 Evaluate side-chains 642 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 582 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 253 ARG Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 253 ARG Chi-restraints excluded: chain O residue 279 SER Chi-restraints excluded: chain O residue 359 SER Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 80 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 182 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 439 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 153 HIS C 96 GLN C 153 HIS C 420 ASN E 96 GLN E 153 HIS G 96 GLN G 153 HIS I 96 GLN I 153 HIS K 96 GLN K 153 HIS M 96 GLN M 153 HIS O 96 GLN O 153 HIS P 133 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.167527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129050 restraints weight = 33228.762| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.67 r_work: 0.3100 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36364 Z= 0.187 Angle : 0.633 9.079 49280 Z= 0.325 Chirality : 0.045 0.174 5208 Planarity : 0.005 0.045 6464 Dihedral : 6.529 59.788 5048 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.89 % Allowed : 9.31 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 4448 helix: 1.08 (0.12), residues: 1648 sheet: -0.72 (0.17), residues: 800 loop : -0.76 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 253 TYR 0.014 0.002 TYR J 67 PHE 0.032 0.002 PHE G 345 TRP 0.009 0.001 TRP D 73 HIS 0.006 0.002 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00442 (36352) covalent geometry : angle 0.62652 (49256) SS BOND : bond 0.01270 ( 12) SS BOND : angle 4.00698 ( 24) hydrogen bonds : bond 0.04052 ( 1496) hydrogen bonds : angle 4.73179 ( 4152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 607 time to evaluate : 1.239 Fit side-chains REVERT: A 52 GLU cc_start: 0.7954 (tp30) cc_final: 0.7684 (mm-30) REVERT: A 205 ASN cc_start: 0.8498 (p0) cc_final: 0.8296 (p0) REVERT: A 253 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8677 (mpt180) REVERT: A 259 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8634 (mm-30) REVERT: A 305 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.7944 (ttp80) REVERT: B 49 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.6831 (mtpt) REVERT: B 80 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7351 (mmt) REVERT: B 111 ASP cc_start: 0.7537 (t0) cc_final: 0.7136 (t0) REVERT: C 52 GLU cc_start: 0.7927 (tp30) cc_final: 0.7656 (mm-30) REVERT: C 180 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8190 (mt) REVERT: C 253 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8661 (mpt180) REVERT: C 259 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8598 (mm-30) REVERT: C 305 ARG cc_start: 0.8517 (ttt-90) cc_final: 0.7924 (ttp80) REVERT: C 339 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7340 (ttm170) REVERT: C 349 MET cc_start: 0.8875 (mtp) cc_final: 0.8554 (mtm) REVERT: D 49 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.6876 (mtpt) REVERT: D 80 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7312 (mmt) REVERT: D 111 ASP cc_start: 0.7553 (t0) cc_final: 0.7218 (t0) REVERT: E 52 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7370 (tm-30) REVERT: E 259 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8619 (mm-30) REVERT: E 305 ARG cc_start: 0.8549 (ttt-90) cc_final: 0.7955 (ttp80) REVERT: E 339 ARG cc_start: 0.8126 (ttp-170) cc_final: 0.7326 (ttm170) REVERT: E 349 MET cc_start: 0.8885 (mtp) cc_final: 0.8568 (mtm) REVERT: F 49 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.6961 (mtpt) REVERT: F 80 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7345 (mmt) REVERT: F 111 ASP cc_start: 0.7569 (t0) cc_final: 0.7189 (t0) REVERT: F 114 LYS cc_start: 0.6201 (ttmt) cc_final: 0.5989 (ttpt) REVERT: F 133 GLN cc_start: 0.8280 (mm-40) cc_final: 0.8060 (mm110) REVERT: G 180 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8198 (mt) REVERT: G 259 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8603 (mm-30) REVERT: G 305 ARG cc_start: 0.8561 (ttt-90) cc_final: 0.7887 (ttp80) REVERT: G 349 MET cc_start: 0.8875 (mtp) cc_final: 0.8548 (mtm) REVERT: H 49 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.6876 (mtpt) REVERT: H 80 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7328 (mmt) REVERT: H 87 MET cc_start: 0.7970 (pmm) cc_final: 0.7446 (pmm) REVERT: H 111 ASP cc_start: 0.7569 (t0) cc_final: 0.7213 (t0) REVERT: H 114 LYS cc_start: 0.6183 (ttmt) cc_final: 0.5977 (ttpt) REVERT: H 133 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8041 (mm110) REVERT: I 52 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7332 (tm-30) REVERT: I 180 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8215 (mt) REVERT: I 259 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8607 (mm-30) REVERT: I 305 ARG cc_start: 0.8533 (ttt-90) cc_final: 0.8302 (ttt180) REVERT: J 49 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.6968 (mtpt) REVERT: J 80 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7328 (mmt) REVERT: J 111 ASP cc_start: 0.7562 (t0) cc_final: 0.7210 (t0) REVERT: J 133 GLN cc_start: 0.8271 (mm-40) cc_final: 0.8046 (mm110) REVERT: K 259 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8586 (mm-30) REVERT: K 305 ARG cc_start: 0.8554 (ttt-90) cc_final: 0.7884 (ttp80) REVERT: K 339 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7310 (ttm170) REVERT: K 349 MET cc_start: 0.8885 (mtp) cc_final: 0.8569 (mtm) REVERT: L 49 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.6860 (mtpt) REVERT: L 80 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7349 (mmt) REVERT: L 111 ASP cc_start: 0.7552 (t0) cc_final: 0.7206 (t0) REVERT: L 133 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8045 (mm110) REVERT: M 52 GLU cc_start: 0.7728 (tp30) cc_final: 0.7301 (mm-30) REVERT: M 203 ASP cc_start: 0.8478 (t70) cc_final: 0.8260 (t70) REVERT: M 205 ASN cc_start: 0.8610 (p0) cc_final: 0.8225 (p0) REVERT: M 253 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8672 (mpt180) REVERT: M 259 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8620 (mm-30) REVERT: M 305 ARG cc_start: 0.8507 (ttt-90) cc_final: 0.7908 (ttp80) REVERT: M 349 MET cc_start: 0.8878 (mtp) cc_final: 0.8583 (mtm) REVERT: N 49 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.6979 (mtpt) REVERT: N 80 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7327 (mmt) REVERT: N 111 ASP cc_start: 0.7554 (t0) cc_final: 0.7166 (t0) REVERT: N 133 GLN cc_start: 0.8267 (mm-40) cc_final: 0.8044 (mm110) REVERT: O 52 GLU cc_start: 0.7813 (tp30) cc_final: 0.7494 (mm-30) REVERT: O 205 ASN cc_start: 0.8609 (p0) cc_final: 0.8231 (p0) REVERT: O 253 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8663 (mpt180) REVERT: O 259 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8606 (mm-30) REVERT: O 305 ARG cc_start: 0.8543 (ttt-90) cc_final: 0.7977 (ttp80) REVERT: P 49 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.6859 (mtpt) REVERT: P 80 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7318 (mmt) REVERT: P 111 ASP cc_start: 0.7540 (t0) cc_final: 0.7191 (t0) REVERT: P 114 LYS cc_start: 0.6188 (ttmt) cc_final: 0.5969 (ttpt) REVERT: P 133 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8272 (mm-40) outliers start: 98 outliers final: 44 residues processed: 674 average time/residue: 0.8729 time to fit residues: 681.0880 Evaluate side-chains 649 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 582 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 253 ARG Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 253 ARG Chi-restraints excluded: chain O residue 359 SER Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 80 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 366 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 384 optimal weight: 5.9990 chunk 359 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 436 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 96 GLN D 133 GLN E 96 GLN G 96 GLN I 96 GLN K 96 GLN M 96 GLN O 96 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.168927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130475 restraints weight = 33075.388| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.66 r_work: 0.3131 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36364 Z= 0.129 Angle : 0.571 7.524 49280 Z= 0.291 Chirality : 0.043 0.169 5208 Planarity : 0.004 0.042 6464 Dihedral : 6.195 58.079 5048 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.78 % Allowed : 10.78 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.12), residues: 4448 helix: 1.59 (0.13), residues: 1656 sheet: -0.42 (0.18), residues: 768 loop : -0.66 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.011 0.001 TYR F 67 PHE 0.030 0.002 PHE G 345 TRP 0.009 0.001 TRP B 73 HIS 0.004 0.001 HIS K 238 Details of bonding type rmsd covalent geometry : bond 0.00296 (36352) covalent geometry : angle 0.56675 (49256) SS BOND : bond 0.00969 ( 12) SS BOND : angle 3.25933 ( 24) hydrogen bonds : bond 0.03461 ( 1496) hydrogen bonds : angle 4.44160 ( 4152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 602 time to evaluate : 1.348 Fit side-chains REVERT: A 52 GLU cc_start: 0.7785 (tp30) cc_final: 0.7510 (mm-30) REVERT: A 205 ASN cc_start: 0.8390 (p0) cc_final: 0.8033 (p0) REVERT: A 259 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8638 (mm-30) REVERT: A 305 ARG cc_start: 0.8496 (ttt-90) cc_final: 0.7922 (ttp80) REVERT: B 49 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7129 (mtpt) REVERT: B 80 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7303 (mmt) REVERT: B 111 ASP cc_start: 0.7539 (t0) cc_final: 0.7025 (t0) REVERT: C 52 GLU cc_start: 0.7928 (tp30) cc_final: 0.7653 (mm-30) REVERT: C 259 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8629 (mm-30) REVERT: C 305 ARG cc_start: 0.8500 (ttt-90) cc_final: 0.7893 (ttp80) REVERT: C 339 ARG cc_start: 0.8098 (ttp-170) cc_final: 0.7331 (ttm170) REVERT: D 49 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7164 (mtpt) REVERT: D 80 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7358 (mmt) REVERT: D 111 ASP cc_start: 0.7546 (t0) cc_final: 0.7097 (t0) REVERT: E 52 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7284 (tm-30) REVERT: E 180 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8223 (mt) REVERT: E 259 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8646 (mm-30) REVERT: E 305 ARG cc_start: 0.8501 (ttt-90) cc_final: 0.7929 (ttp80) REVERT: E 339 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7329 (ttm170) REVERT: F 49 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7139 (mtpt) REVERT: F 80 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7365 (mmt) REVERT: F 111 ASP cc_start: 0.7567 (t0) cc_final: 0.7188 (t0) REVERT: F 133 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8137 (mm110) REVERT: G 180 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8383 (mt) REVERT: G 259 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8632 (mm-30) REVERT: G 305 ARG cc_start: 0.8503 (ttt-90) cc_final: 0.7815 (ttp80) REVERT: H 49 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7153 (mtpt) REVERT: H 80 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7323 (mmt) REVERT: H 87 MET cc_start: 0.8001 (pmm) cc_final: 0.7413 (pmm) REVERT: H 111 ASP cc_start: 0.7563 (t0) cc_final: 0.7130 (t0) REVERT: H 114 LYS cc_start: 0.6140 (ttmt) cc_final: 0.5893 (ttpt) REVERT: I 52 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7324 (tm-30) REVERT: I 259 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8618 (mm-30) REVERT: I 305 ARG cc_start: 0.8511 (ttt-90) cc_final: 0.8200 (ttt180) REVERT: J 49 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7136 (mtpt) REVERT: J 80 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7357 (mmt) REVERT: J 111 ASP cc_start: 0.7565 (t0) cc_final: 0.7105 (t0) REVERT: J 133 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8132 (mm110) REVERT: K 52 GLU cc_start: 0.7804 (tp30) cc_final: 0.7354 (mm-30) REVERT: K 180 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8187 (mt) REVERT: K 259 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8655 (mm-30) REVERT: K 305 ARG cc_start: 0.8535 (ttt-90) cc_final: 0.7851 (ttp80) REVERT: K 339 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7314 (ttm170) REVERT: L 49 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7140 (mtpt) REVERT: L 80 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7308 (mmt) REVERT: L 111 ASP cc_start: 0.7568 (t0) cc_final: 0.7086 (t0) REVERT: L 133 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8068 (mm110) REVERT: M 52 GLU cc_start: 0.7720 (tp30) cc_final: 0.7290 (mm-30) REVERT: M 180 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8226 (mt) REVERT: M 205 ASN cc_start: 0.8536 (p0) cc_final: 0.8013 (p0) REVERT: M 259 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8638 (mm-30) REVERT: M 305 ARG cc_start: 0.8500 (ttt-90) cc_final: 0.7887 (ttp80) REVERT: N 49 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7182 (mtpt) REVERT: N 80 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7341 (mmt) REVERT: N 111 ASP cc_start: 0.7549 (t0) cc_final: 0.7140 (t0) REVERT: N 133 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8112 (mm110) REVERT: O 52 GLU cc_start: 0.7803 (tp30) cc_final: 0.7438 (mm-30) REVERT: O 180 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8218 (mt) REVERT: O 203 ASP cc_start: 0.8535 (t70) cc_final: 0.8303 (t0) REVERT: O 205 ASN cc_start: 0.8463 (p0) cc_final: 0.8227 (p0) REVERT: O 259 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8653 (mm-30) REVERT: O 305 ARG cc_start: 0.8523 (ttt-90) cc_final: 0.7952 (ttp80) REVERT: O 339 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7455 (ttm170) REVERT: P 49 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7151 (mtpt) REVERT: P 80 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7350 (mmt) REVERT: P 111 ASP cc_start: 0.7536 (t0) cc_final: 0.7124 (t0) REVERT: P 133 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8177 (mm-40) outliers start: 94 outliers final: 55 residues processed: 661 average time/residue: 0.8986 time to fit residues: 685.4473 Evaluate side-chains 652 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 576 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 369 CYS Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 253 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 369 CYS Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 253 ARG Chi-restraints excluded: chain K residue 369 CYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 369 CYS Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 359 SER Chi-restraints excluded: chain O residue 369 CYS Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 80 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 310 optimal weight: 7.9990 chunk 349 optimal weight: 4.9990 chunk 433 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 358 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 96 GLN E 96 GLN G 96 GLN I 96 GLN K 96 GLN M 96 GLN O 96 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.165985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127414 restraints weight = 33077.672| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.59 r_work: 0.3070 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 36364 Z= 0.242 Angle : 0.670 8.492 49280 Z= 0.343 Chirality : 0.047 0.181 5208 Planarity : 0.005 0.045 6464 Dihedral : 6.425 57.612 5048 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.64 % Allowed : 11.90 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4448 helix: 1.46 (0.13), residues: 1656 sheet: -0.49 (0.18), residues: 760 loop : -0.70 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 71 TYR 0.013 0.002 TYR E 269 PHE 0.031 0.003 PHE G 345 TRP 0.008 0.001 TRP N 73 HIS 0.007 0.002 HIS M 292 Details of bonding type rmsd covalent geometry : bond 0.00577 (36352) covalent geometry : angle 0.66400 (49256) SS BOND : bond 0.01462 ( 12) SS BOND : angle 4.14651 ( 24) hydrogen bonds : bond 0.04359 ( 1496) hydrogen bonds : angle 4.62917 ( 4152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 581 time to evaluate : 1.215 Fit side-chains REVERT: A 52 GLU cc_start: 0.7911 (tp30) cc_final: 0.7637 (mm-30) REVERT: A 205 ASN cc_start: 0.8512 (p0) cc_final: 0.8290 (p0) REVERT: A 259 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8683 (mm-30) REVERT: A 305 ARG cc_start: 0.8566 (ttt-90) cc_final: 0.7967 (ttp80) REVERT: B 49 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7071 (mtpt) REVERT: B 80 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7483 (mmt) REVERT: B 111 ASP cc_start: 0.7618 (t0) cc_final: 0.7186 (t0) REVERT: B 133 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8016 (mm110) REVERT: C 52 GLU cc_start: 0.7933 (tp30) cc_final: 0.7605 (mm-30) REVERT: C 259 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8647 (mm-30) REVERT: C 305 ARG cc_start: 0.8604 (ttt-90) cc_final: 0.7981 (ttp80) REVERT: C 339 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7318 (ttm170) REVERT: D 49 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7096 (mtpt) REVERT: D 80 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7414 (mmt) REVERT: D 111 ASP cc_start: 0.7655 (t0) cc_final: 0.7187 (t0) REVERT: E 259 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8657 (mm-30) REVERT: E 305 ARG cc_start: 0.8583 (ttt-90) cc_final: 0.7973 (ttp80) REVERT: E 339 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7332 (ttm170) REVERT: F 49 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7082 (mtpt) REVERT: F 80 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7474 (mmt) REVERT: F 111 ASP cc_start: 0.7727 (t0) cc_final: 0.7240 (t0) REVERT: G 259 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8663 (mm-30) REVERT: G 305 ARG cc_start: 0.8607 (ttt-90) cc_final: 0.7912 (ttp80) REVERT: H 49 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.6889 (mtpt) REVERT: H 80 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7444 (mmt) REVERT: H 87 MET cc_start: 0.8014 (pmm) cc_final: 0.7427 (pmm) REVERT: H 111 ASP cc_start: 0.7658 (t0) cc_final: 0.7152 (t0) REVERT: H 114 LYS cc_start: 0.6231 (ttmt) cc_final: 0.5902 (ttpt) REVERT: I 259 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8653 (mm-30) REVERT: I 305 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.8324 (ttt180) REVERT: J 49 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7062 (mtpt) REVERT: J 80 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7443 (mmt) REVERT: J 111 ASP cc_start: 0.7719 (t0) cc_final: 0.7238 (t0) REVERT: K 259 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8653 (mm-30) REVERT: K 305 ARG cc_start: 0.8587 (ttt-90) cc_final: 0.7889 (ttp80) REVERT: K 339 ARG cc_start: 0.8104 (ttp-170) cc_final: 0.7303 (ttm170) REVERT: L 49 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7086 (mtpt) REVERT: L 80 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7454 (mmt) REVERT: L 111 ASP cc_start: 0.7651 (t0) cc_final: 0.7205 (t0) REVERT: M 52 GLU cc_start: 0.7739 (tp30) cc_final: 0.7301 (mm-30) REVERT: M 203 ASP cc_start: 0.8496 (t70) cc_final: 0.8269 (t0) REVERT: M 205 ASN cc_start: 0.8538 (p0) cc_final: 0.8318 (p0) REVERT: M 259 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8647 (mm-30) REVERT: M 305 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.7979 (ttp80) REVERT: N 49 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7111 (mtpt) REVERT: N 80 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7545 (mmt) REVERT: N 111 ASP cc_start: 0.7649 (t0) cc_final: 0.7168 (t0) REVERT: O 52 GLU cc_start: 0.7825 (tp30) cc_final: 0.7489 (mm-30) REVERT: O 203 ASP cc_start: 0.8477 (t70) cc_final: 0.8262 (t0) REVERT: O 205 ASN cc_start: 0.8586 (p0) cc_final: 0.8360 (p0) REVERT: O 259 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8679 (mm-30) REVERT: P 49 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7087 (mtpt) REVERT: P 80 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7510 (mmt) REVERT: P 111 ASP cc_start: 0.7699 (t0) cc_final: 0.7249 (t0) outliers start: 89 outliers final: 60 residues processed: 638 average time/residue: 0.8839 time to fit residues: 651.2112 Evaluate side-chains 634 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 558 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 369 CYS Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 253 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 369 CYS Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 253 ARG Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 369 CYS Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 369 CYS Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 359 SER Chi-restraints excluded: chain O residue 369 CYS Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 80 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 63 optimal weight: 3.9990 chunk 425 optimal weight: 20.0000 chunk 237 optimal weight: 0.3980 chunk 217 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 371 optimal weight: 0.5980 chunk 284 optimal weight: 10.0000 chunk 381 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 410 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 96 GLN E 96 GLN G 96 GLN I 96 GLN K 96 GLN M 96 GLN O 96 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.168687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130394 restraints weight = 33153.056| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.62 r_work: 0.3128 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36364 Z= 0.122 Angle : 0.563 7.601 49280 Z= 0.287 Chirality : 0.042 0.172 5208 Planarity : 0.004 0.041 6464 Dihedral : 6.118 55.962 5048 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.42 % Allowed : 12.75 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.12), residues: 4448 helix: 1.83 (0.13), residues: 1656 sheet: -0.34 (0.18), residues: 768 loop : -0.58 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 305 TYR 0.013 0.001 TYR G 29 PHE 0.030 0.002 PHE G 345 TRP 0.007 0.001 TRP B 73 HIS 0.005 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00276 (36352) covalent geometry : angle 0.55915 (49256) SS BOND : bond 0.00963 ( 12) SS BOND : angle 3.19219 ( 24) hydrogen bonds : bond 0.03395 ( 1496) hydrogen bonds : angle 4.37314 ( 4152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 574 time to evaluate : 1.396 Fit side-chains REVERT: A 52 GLU cc_start: 0.7767 (tp30) cc_final: 0.7462 (mm-30) REVERT: A 205 ASN cc_start: 0.8435 (p0) cc_final: 0.8024 (p0) REVERT: A 259 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8672 (mm-30) REVERT: A 305 ARG cc_start: 0.8517 (ttt-90) cc_final: 0.7935 (ttp80) REVERT: B 49 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7136 (mtpt) REVERT: B 80 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7375 (mmt) REVERT: B 111 ASP cc_start: 0.7483 (t0) cc_final: 0.6973 (t0) REVERT: C 52 GLU cc_start: 0.7941 (tp30) cc_final: 0.7617 (mm-30) REVERT: C 259 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8658 (mm-30) REVERT: C 305 ARG cc_start: 0.8532 (ttt-90) cc_final: 0.7906 (ttp80) REVERT: C 339 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7318 (ttm170) REVERT: D 49 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7182 (mtpt) REVERT: D 80 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7309 (mmt) REVERT: D 111 ASP cc_start: 0.7530 (t0) cc_final: 0.6991 (t0) REVERT: E 52 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7584 (tm-30) REVERT: E 259 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8650 (mm-30) REVERT: E 305 ARG cc_start: 0.8522 (ttt-90) cc_final: 0.7925 (ttp80) REVERT: E 339 ARG cc_start: 0.8102 (ttp-170) cc_final: 0.7342 (ttm170) REVERT: F 49 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7149 (mtpt) REVERT: F 80 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7317 (mmt) REVERT: F 111 ASP cc_start: 0.7630 (t0) cc_final: 0.7115 (t0) REVERT: G 259 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8673 (mm-30) REVERT: G 305 ARG cc_start: 0.8532 (ttt-90) cc_final: 0.7904 (ttp80) REVERT: H 49 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.7175 (mtpt) REVERT: H 80 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7255 (mmt) REVERT: H 87 MET cc_start: 0.8041 (pmm) cc_final: 0.7478 (pmm) REVERT: H 111 ASP cc_start: 0.7597 (t0) cc_final: 0.7159 (t0) REVERT: H 114 LYS cc_start: 0.6315 (ttmt) cc_final: 0.6047 (ttpt) REVERT: H 133 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8069 (mm110) REVERT: I 52 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7595 (tm-30) REVERT: I 259 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8644 (mm-30) REVERT: I 305 ARG cc_start: 0.8548 (ttt-90) cc_final: 0.8248 (ttt180) REVERT: J 49 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7143 (mtpt) REVERT: J 80 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7313 (mmt) REVERT: J 111 ASP cc_start: 0.7621 (t0) cc_final: 0.7122 (t0) REVERT: K 52 GLU cc_start: 0.7954 (tp30) cc_final: 0.7469 (mm-30) REVERT: K 259 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8662 (mm-30) REVERT: K 305 ARG cc_start: 0.8547 (ttt-90) cc_final: 0.7856 (ttp80) REVERT: K 339 ARG cc_start: 0.8086 (ttp-170) cc_final: 0.7311 (ttm170) REVERT: L 49 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7158 (mtpt) REVERT: L 80 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7347 (mmt) REVERT: L 111 ASP cc_start: 0.7546 (t0) cc_final: 0.7054 (t0) REVERT: M 52 GLU cc_start: 0.7743 (tp30) cc_final: 0.7311 (mm-30) REVERT: M 205 ASN cc_start: 0.8481 (p0) cc_final: 0.8087 (p0) REVERT: M 259 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8650 (mm-30) REVERT: M 305 ARG cc_start: 0.8533 (ttt-90) cc_final: 0.7901 (ttp80) REVERT: N 49 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7182 (mtpt) REVERT: N 80 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7407 (mmt) REVERT: N 111 ASP cc_start: 0.7535 (t0) cc_final: 0.7026 (t0) REVERT: O 52 GLU cc_start: 0.7930 (tp30) cc_final: 0.7583 (mm-30) REVERT: O 205 ASN cc_start: 0.8467 (p0) cc_final: 0.8044 (p0) REVERT: O 259 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8684 (mm-30) REVERT: O 305 ARG cc_start: 0.8556 (ttt-90) cc_final: 0.7982 (ttp80) REVERT: O 339 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7526 (ttm170) REVERT: P 49 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7174 (mtpt) REVERT: P 80 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7371 (mmt) REVERT: P 111 ASP cc_start: 0.7588 (t0) cc_final: 0.7153 (t0) outliers start: 81 outliers final: 62 residues processed: 633 average time/residue: 0.8957 time to fit residues: 654.7199 Evaluate side-chains 629 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 551 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 369 CYS Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 253 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 369 CYS Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 51 TYR Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 253 ARG Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 369 CYS Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 369 CYS Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 51 TYR Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 369 CYS Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 80 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 243 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 352 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 153 HIS A 156 GLN C 96 GLN C 153 HIS E 96 GLN E 156 GLN F 133 GLN G 96 GLN G 153 HIS I 96 GLN I 153 HIS J 133 GLN K 96 GLN K 153 HIS L 133 GLN M 96 GLN M 153 HIS O 96 GLN O 153 HIS O 156 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.164085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125596 restraints weight = 33289.755| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.60 r_work: 0.3061 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 36364 Z= 0.356 Angle : 0.776 9.014 49280 Z= 0.398 Chirality : 0.053 0.207 5208 Planarity : 0.006 0.064 6464 Dihedral : 6.635 56.402 5048 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.75 % Allowed : 12.50 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 4448 helix: 1.38 (0.12), residues: 1648 sheet: -0.70 (0.18), residues: 800 loop : -0.64 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 71 TYR 0.018 0.003 TYR P 68 PHE 0.032 0.004 PHE C 345 TRP 0.012 0.002 TRP M 385 HIS 0.009 0.003 HIS I 238 Details of bonding type rmsd covalent geometry : bond 0.00851 (36352) covalent geometry : angle 0.76859 (49256) SS BOND : bond 0.01854 ( 12) SS BOND : angle 4.81140 ( 24) hydrogen bonds : bond 0.05145 ( 1496) hydrogen bonds : angle 4.83065 ( 4152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 544 time to evaluate : 1.049 Fit side-chains REVERT: A 203 ASP cc_start: 0.8432 (t70) cc_final: 0.8139 (t0) REVERT: A 259 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8568 (mm-30) REVERT: B 49 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.6878 (mtpt) REVERT: B 80 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7519 (mmt) REVERT: B 111 ASP cc_start: 0.7683 (t0) cc_final: 0.7260 (t0) REVERT: C 52 GLU cc_start: 0.7900 (tp30) cc_final: 0.7593 (mm-30) REVERT: C 203 ASP cc_start: 0.8411 (t70) cc_final: 0.8197 (t0) REVERT: C 259 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8546 (mm-30) REVERT: C 305 ARG cc_start: 0.8578 (ttt-90) cc_final: 0.7966 (ttp80) REVERT: C 339 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7310 (ttm170) REVERT: D 49 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.6895 (mtpt) REVERT: D 80 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7517 (mmt) REVERT: D 111 ASP cc_start: 0.7726 (t0) cc_final: 0.7246 (t0) REVERT: E 253 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.7281 (mpt180) REVERT: E 259 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8544 (mm-30) REVERT: E 305 ARG cc_start: 0.8566 (ttt-90) cc_final: 0.7976 (ttp80) REVERT: E 339 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7341 (ttm170) REVERT: F 49 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.6888 (mtpt) REVERT: F 80 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7446 (mmt) REVERT: F 111 ASP cc_start: 0.7798 (t0) cc_final: 0.7390 (t0) REVERT: G 259 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8543 (mm-30) REVERT: G 305 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.7900 (ttp80) REVERT: H 49 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7783 (mmtt) REVERT: H 80 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7575 (mmt) REVERT: H 87 MET cc_start: 0.8071 (pmm) cc_final: 0.7446 (pmm) REVERT: H 111 ASP cc_start: 0.7693 (t0) cc_final: 0.7328 (t0) REVERT: H 114 LYS cc_start: 0.6483 (ttmt) cc_final: 0.6207 (ttpt) REVERT: I 203 ASP cc_start: 0.8384 (t70) cc_final: 0.8164 (t0) REVERT: I 259 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8546 (mm-30) REVERT: J 49 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.6864 (mtpt) REVERT: J 80 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7525 (mmt) REVERT: J 102 ASP cc_start: 0.8629 (m-30) cc_final: 0.8272 (m-30) REVERT: J 111 ASP cc_start: 0.7780 (t0) cc_final: 0.7374 (t0) REVERT: K 52 GLU cc_start: 0.7945 (tp30) cc_final: 0.7297 (mm-30) REVERT: K 253 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.7243 (mpt180) REVERT: K 259 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8548 (mm-30) REVERT: K 305 ARG cc_start: 0.8589 (ttt-90) cc_final: 0.7885 (ttp80) REVERT: K 339 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7294 (ttm170) REVERT: L 49 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.6888 (mtpt) REVERT: L 80 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7515 (mmt) REVERT: L 111 ASP cc_start: 0.7699 (t0) cc_final: 0.7211 (t0) REVERT: M 203 ASP cc_start: 0.8539 (t70) cc_final: 0.8287 (t0) REVERT: M 205 ASN cc_start: 0.8642 (p0) cc_final: 0.8440 (p0) REVERT: M 259 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8547 (mm-30) REVERT: M 443 ASP cc_start: 0.7679 (m-30) cc_final: 0.7461 (OUTLIER) REVERT: N 49 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.6884 (mtpt) REVERT: N 80 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7509 (mmt) REVERT: N 111 ASP cc_start: 0.7767 (t0) cc_final: 0.7303 (t0) REVERT: O 52 GLU cc_start: 0.7773 (tp30) cc_final: 0.7424 (mm-30) REVERT: O 203 ASP cc_start: 0.8525 (t70) cc_final: 0.8277 (t0) REVERT: O 205 ASN cc_start: 0.8659 (p0) cc_final: 0.8450 (p0) REVERT: O 259 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8582 (mm-30) REVERT: O 305 ARG cc_start: 0.8561 (ttt-90) cc_final: 0.7923 (ttp80) REVERT: P 49 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.6908 (mtpt) REVERT: P 80 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7528 (mmt) REVERT: P 111 ASP cc_start: 0.7750 (t0) cc_final: 0.7328 (t0) outliers start: 93 outliers final: 63 residues processed: 607 average time/residue: 0.9085 time to fit residues: 636.2777 Evaluate side-chains 612 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 530 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 369 CYS Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 253 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 369 CYS Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 253 ARG Chi-restraints excluded: chain K residue 297 MET Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 369 CYS Chi-restraints excluded: chain K residue 371 MET Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 253 ARG Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 369 CYS Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 253 ARG Chi-restraints excluded: chain O residue 359 SER Chi-restraints excluded: chain O residue 369 CYS Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 80 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 4 optimal weight: 9.9990 chunk 405 optimal weight: 1.9990 chunk 365 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 281 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 242 optimal weight: 0.7980 chunk 254 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 260 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 153 HIS A 156 GLN C 96 GLN C 153 HIS E 96 GLN E 156 GLN G 96 GLN G 153 HIS I 96 GLN I 153 HIS K 96 GLN K 153 HIS M 96 GLN M 153 HIS O 96 GLN O 153 HIS O 156 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.166962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128472 restraints weight = 33162.745| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.66 r_work: 0.3116 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36364 Z= 0.154 Angle : 0.604 8.124 49280 Z= 0.309 Chirality : 0.044 0.178 5208 Planarity : 0.004 0.045 6464 Dihedral : 6.282 56.190 5048 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.61 % Allowed : 12.72 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 4448 helix: 1.75 (0.13), residues: 1648 sheet: -0.40 (0.18), residues: 768 loop : -0.66 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 83 TYR 0.015 0.002 TYR I 29 PHE 0.031 0.002 PHE G 345 TRP 0.007 0.001 TRP M 385 HIS 0.006 0.001 HIS E 153 Details of bonding type rmsd covalent geometry : bond 0.00359 (36352) covalent geometry : angle 0.59871 (49256) SS BOND : bond 0.01142 ( 12) SS BOND : angle 3.59322 ( 24) hydrogen bonds : bond 0.03740 ( 1496) hydrogen bonds : angle 4.47641 ( 4152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 560 time to evaluate : 1.406 Fit side-chains REVERT: A 205 ASN cc_start: 0.8630 (p0) cc_final: 0.8401 (p0) REVERT: A 259 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8605 (mm-30) REVERT: A 305 ARG cc_start: 0.8535 (ttt-90) cc_final: 0.7973 (ttp80) REVERT: A 339 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7670 (ttm170) REVERT: A 425 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8344 (mt-10) REVERT: B 49 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7164 (mtpt) REVERT: B 80 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7276 (mmt) REVERT: B 111 ASP cc_start: 0.7594 (t0) cc_final: 0.7134 (t0) REVERT: C 52 GLU cc_start: 0.7926 (tp30) cc_final: 0.7600 (mm-30) REVERT: C 259 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8563 (mm-30) REVERT: C 305 ARG cc_start: 0.8524 (ttt-90) cc_final: 0.7916 (ttp80) REVERT: C 339 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7337 (ttm170) REVERT: C 425 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8352 (mt-10) REVERT: D 49 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7198 (mtpt) REVERT: D 80 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7260 (mmt) REVERT: D 111 ASP cc_start: 0.7569 (t0) cc_final: 0.7095 (t0) REVERT: E 259 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8567 (mm-30) REVERT: E 305 ARG cc_start: 0.8524 (ttt-90) cc_final: 0.7929 (ttp80) REVERT: E 339 ARG cc_start: 0.8112 (ttp-170) cc_final: 0.7372 (ttm170) REVERT: F 49 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7170 (mtpt) REVERT: F 80 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7280 (mmt) REVERT: F 111 ASP cc_start: 0.7671 (t0) cc_final: 0.7211 (t0) REVERT: G 259 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8581 (mm-30) REVERT: G 305 ARG cc_start: 0.8542 (ttt-90) cc_final: 0.7943 (ttp80) REVERT: H 49 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.7201 (mtpt) REVERT: H 80 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7319 (mmt) REVERT: H 87 MET cc_start: 0.8013 (pmm) cc_final: 0.7442 (pmm) REVERT: H 111 ASP cc_start: 0.7641 (t0) cc_final: 0.7260 (t0) REVERT: H 114 LYS cc_start: 0.6364 (ttmt) cc_final: 0.6157 (ttpt) REVERT: I 259 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8555 (mm-30) REVERT: I 305 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.8230 (ttt180) REVERT: J 49 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7168 (mtpt) REVERT: J 80 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7245 (mmt) REVERT: J 111 ASP cc_start: 0.7668 (t0) cc_final: 0.7174 (t0) REVERT: K 52 GLU cc_start: 0.7964 (tp30) cc_final: 0.7307 (mm-30) REVERT: K 259 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8573 (mm-30) REVERT: K 305 ARG cc_start: 0.8548 (ttt-90) cc_final: 0.7947 (ttp80) REVERT: K 339 ARG cc_start: 0.8083 (ttp-170) cc_final: 0.7313 (ttm170) REVERT: L 49 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.7174 (mtpt) REVERT: L 80 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7250 (mmt) REVERT: L 111 ASP cc_start: 0.7572 (t0) cc_final: 0.7196 (t0) REVERT: M 52 GLU cc_start: 0.7725 (tp30) cc_final: 0.6906 (tm-30) REVERT: M 203 ASP cc_start: 0.8512 (t70) cc_final: 0.8256 (t0) REVERT: M 205 ASN cc_start: 0.8591 (p0) cc_final: 0.8367 (p0) REVERT: M 259 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8564 (mm-30) REVERT: M 305 ARG cc_start: 0.8486 (ttt-90) cc_final: 0.7919 (ttp80) REVERT: M 425 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8341 (mt-10) REVERT: N 49 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7192 (mtpt) REVERT: N 80 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7324 (mmt) REVERT: N 111 ASP cc_start: 0.7568 (t0) cc_final: 0.7068 (t0) REVERT: O 52 GLU cc_start: 0.7920 (tp30) cc_final: 0.7661 (mm-30) REVERT: O 203 ASP cc_start: 0.8515 (t70) cc_final: 0.8275 (t0) REVERT: O 205 ASN cc_start: 0.8588 (p0) cc_final: 0.8374 (p0) REVERT: O 259 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8593 (mm-30) REVERT: O 305 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.7946 (ttp80) REVERT: O 425 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8350 (mt-10) REVERT: P 49 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7184 (mtpt) REVERT: P 80 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7298 (mmt) REVERT: P 111 ASP cc_start: 0.7648 (t0) cc_final: 0.7266 (t0) outliers start: 88 outliers final: 62 residues processed: 627 average time/residue: 0.9104 time to fit residues: 659.3963 Evaluate side-chains 622 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 544 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 369 CYS Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 371 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 253 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 369 CYS Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 253 ARG Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 369 CYS Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 253 ARG Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 369 CYS Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 253 ARG Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 369 CYS Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 406 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 385 optimal weight: 20.0000 chunk 383 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 433 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 156 GLN C 96 GLN E 96 GLN E 156 GLN G 96 GLN I 96 GLN K 96 GLN M 96 GLN O 96 GLN O 156 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.166159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127504 restraints weight = 33237.729| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.67 r_work: 0.3103 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36364 Z= 0.187 Angle : 0.635 8.223 49280 Z= 0.324 Chirality : 0.045 0.181 5208 Planarity : 0.005 0.045 6464 Dihedral : 6.298 56.014 5048 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.56 % Allowed : 12.99 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.12), residues: 4448 helix: 1.68 (0.13), residues: 1656 sheet: -0.36 (0.18), residues: 768 loop : -0.63 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 421 TYR 0.017 0.002 TYR E 29 PHE 0.030 0.002 PHE G 345 TRP 0.007 0.001 TRP F 73 HIS 0.007 0.002 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00442 (36352) covalent geometry : angle 0.62929 (49256) SS BOND : bond 0.01278 ( 12) SS BOND : angle 3.80272 ( 24) hydrogen bonds : bond 0.03990 ( 1496) hydrogen bonds : angle 4.50643 ( 4152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 551 time to evaluate : 1.362 Fit side-chains REVERT: A 205 ASN cc_start: 0.8600 (p0) cc_final: 0.8385 (p0) REVERT: A 259 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8631 (mm-30) REVERT: A 305 ARG cc_start: 0.8518 (ttt-90) cc_final: 0.7970 (ttp80) REVERT: B 49 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7072 (mtpt) REVERT: B 80 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7380 (mmt) REVERT: B 111 ASP cc_start: 0.7554 (t0) cc_final: 0.7037 (t0) REVERT: C 52 GLU cc_start: 0.7934 (tp30) cc_final: 0.7607 (mm-30) REVERT: C 259 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8607 (mm-30) REVERT: C 305 ARG cc_start: 0.8554 (ttt-90) cc_final: 0.7942 (ttp80) REVERT: C 339 ARG cc_start: 0.8120 (ttp-170) cc_final: 0.7323 (ttm170) REVERT: D 49 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7112 (mtpt) REVERT: D 80 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7354 (mmt) REVERT: D 111 ASP cc_start: 0.7594 (t0) cc_final: 0.7213 (t0) REVERT: E 259 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8589 (mm-30) REVERT: E 305 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.7931 (ttp80) REVERT: E 339 ARG cc_start: 0.8106 (ttp-170) cc_final: 0.7356 (ttm170) REVERT: F 49 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7076 (mtpt) REVERT: F 80 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7464 (mmt) REVERT: F 111 ASP cc_start: 0.7690 (t0) cc_final: 0.7329 (t0) REVERT: G 259 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8609 (mm-30) REVERT: G 305 ARG cc_start: 0.8558 (ttt-90) cc_final: 0.7868 (ttp80) REVERT: H 49 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.7125 (mtpt) REVERT: H 80 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7413 (mmt) REVERT: H 87 MET cc_start: 0.8055 (pmm) cc_final: 0.7461 (pmm) REVERT: H 111 ASP cc_start: 0.7654 (t0) cc_final: 0.7218 (t0) REVERT: H 114 LYS cc_start: 0.6384 (ttmt) cc_final: 0.6128 (ttpt) REVERT: I 259 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8579 (mm-30) REVERT: I 305 ARG cc_start: 0.8548 (ttt-90) cc_final: 0.8245 (ttt180) REVERT: J 49 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7083 (mtpt) REVERT: J 80 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7448 (mmt) REVERT: J 111 ASP cc_start: 0.7699 (t0) cc_final: 0.7241 (t0) REVERT: K 52 GLU cc_start: 0.7961 (tp30) cc_final: 0.7302 (mm-30) REVERT: K 259 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8605 (mm-30) REVERT: K 305 ARG cc_start: 0.8571 (ttt-90) cc_final: 0.7876 (ttp80) REVERT: K 339 ARG cc_start: 0.8094 (ttp-170) cc_final: 0.7323 (ttm170) REVERT: L 49 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7092 (mtpt) REVERT: L 80 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7372 (mmt) REVERT: L 111 ASP cc_start: 0.7603 (t0) cc_final: 0.7226 (t0) REVERT: M 52 GLU cc_start: 0.7726 (tp30) cc_final: 0.6905 (tm-30) REVERT: M 203 ASP cc_start: 0.8518 (t70) cc_final: 0.8269 (t0) REVERT: M 205 ASN cc_start: 0.8581 (p0) cc_final: 0.8363 (p0) REVERT: M 259 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8597 (mm-30) REVERT: M 305 ARG cc_start: 0.8500 (ttt-90) cc_final: 0.7921 (ttp80) REVERT: N 49 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7093 (mtpt) REVERT: N 80 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7426 (mmt) REVERT: N 111 ASP cc_start: 0.7590 (t0) cc_final: 0.7179 (t0) REVERT: O 52 GLU cc_start: 0.7918 (tp30) cc_final: 0.7612 (mm-30) REVERT: O 203 ASP cc_start: 0.8508 (t70) cc_final: 0.8249 (t0) REVERT: O 205 ASN cc_start: 0.8611 (p0) cc_final: 0.8377 (p0) REVERT: O 259 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8616 (mm-30) REVERT: O 305 ARG cc_start: 0.8514 (ttt-90) cc_final: 0.7947 (ttp80) REVERT: P 49 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7099 (mtpt) REVERT: P 80 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7395 (mmt) REVERT: P 111 ASP cc_start: 0.7665 (t0) cc_final: 0.7228 (t0) outliers start: 86 outliers final: 65 residues processed: 611 average time/residue: 0.8822 time to fit residues: 623.3795 Evaluate side-chains 621 residues out of total 3688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 540 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 369 CYS Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 369 CYS Chi-restraints excluded: chain G residue 371 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 253 ARG Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 369 CYS Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 253 ARG Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 369 CYS Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 253 ARG Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 369 CYS Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 253 ARG Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 359 SER Chi-restraints excluded: chain O residue 369 CYS Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 238 optimal weight: 1.9990 chunk 356 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 407 optimal weight: 0.1980 chunk 205 optimal weight: 8.9990 chunk 43 optimal weight: 0.0010 chunk 413 optimal weight: 7.9990 chunk 266 optimal weight: 3.9990 overall best weight: 2.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 156 GLN C 96 GLN E 96 GLN E 156 GLN G 96 GLN I 96 GLN K 96 GLN M 96 GLN O 96 GLN O 156 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.167448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129146 restraints weight = 33108.383| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.62 r_work: 0.3121 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 36364 Z= 0.152 Angle : 0.600 8.025 49280 Z= 0.306 Chirality : 0.044 0.178 5208 Planarity : 0.004 0.043 6464 Dihedral : 6.181 56.776 5048 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.72 % Allowed : 12.96 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.12), residues: 4448 helix: 1.85 (0.13), residues: 1656 sheet: -0.30 (0.18), residues: 768 loop : -0.59 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 421 TYR 0.017 0.002 TYR I 29 PHE 0.030 0.002 PHE A 345 TRP 0.007 0.001 TRP F 73 HIS 0.006 0.001 HIS E 153 Details of bonding type rmsd covalent geometry : bond 0.00354 (36352) covalent geometry : angle 0.59509 (49256) SS BOND : bond 0.01082 ( 12) SS BOND : angle 3.40568 ( 24) hydrogen bonds : bond 0.03676 ( 1496) hydrogen bonds : angle 4.40927 ( 4152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15457.85 seconds wall clock time: 262 minutes 48.29 seconds (15768.29 seconds total)